Ben Bolstad
| Snapshot Date: 2024-06-26 14:00 -0400 (Wed, 26 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_19 |
| git_last_commit: af6c73d |
| git_last_commit_date: 2024-04-30 10:16:21 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-28 17:46 -0400 (Fri, 28 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4494 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4508 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4362 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 249/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.68.0 (landing page) Ben Bolstad
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.68.0 |
| Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BufferedMatrix_1.68.0.tar.gz |
| StartedAt: 2024-06-26 23:41:48 -0400 (Wed, 26 Jun 2024) |
| EndedAt: 2024-06-26 23:43:02 -0400 (Wed, 26 Jun 2024) |
| EllapsedTime: 74.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:BufferedMatrix.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings BufferedMatrix_1.68.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'BufferedMatrix/DESCRIPTION' ... OK
* this is package 'BufferedMatrix' version '1.68.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BufferedMatrix' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/BufferedMatrix/libs/x64/BufferedMatrix.dll':
Found '_exit', possibly from '_exit' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... NONE
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'Rcodetesting.R'
Running 'c_code_level_tests.R'
Running 'objectTesting.R'
Running 'rawCalltesting.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/00check.log'
for details.
BufferedMatrix.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'BufferedMatrix' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"c:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"c:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function 'dbm_ReadOnlyMode':
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of '!' or change '&' to '&&' or '!' to '~' [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: 'sort_double' defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"c:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG -I"c:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c init_package.c -o init_package.o
gcc -shared -s -static-libgcc -o BufferedMatrix.dll tmp.def RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -Lc:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'rowMeans' in package 'BufferedMatrix'
Creating a new generic function for 'rowSums' in package 'BufferedMatrix'
Creating a new generic function for 'colMeans' in package 'BufferedMatrix'
Creating a new generic function for 'colSums' in package 'BufferedMatrix'
Creating a generic function for 'ncol' from package 'base' in package 'BufferedMatrix'
Creating a generic function for 'nrow' from package 'base' in package 'BufferedMatrix'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.32 0.12 0.64
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 468463 25.1 1021758 54.6 633414 33.9
Vcells 853871 6.6 8388608 64.0 2003098 15.3
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Wed Jun 26 23:42:17 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Wed Jun 26 23:42:17 2024"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x000001d23d6ff3b0>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Wed Jun 26 23:42:24 2024"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Wed Jun 26 23:42:26 2024"
>
> ColMode(tmp2)
<pointer: 0x000001d23d6ff3b0>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.143396 1.8832468 -0.6768216 -0.4327710
[2,] -0.472305 0.8225508 1.6844578 -0.9664929
[3,] -1.184838 -0.9703975 -0.4779062 -0.2917089
[4,] -0.101914 1.1771228 0.9199079 -0.7720828
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 100.143396 1.8832468 0.6768216 0.4327710
[2,] 0.472305 0.8225508 1.6844578 0.9664929
[3,] 1.184838 0.9703975 0.4779062 0.2917089
[4,] 0.101914 1.1771228 0.9199079 0.7720828
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 10.0071673 1.3723144 0.8226917 0.6578533
[2,] 0.6872445 0.9069459 1.2978667 0.9831037
[3,] 1.0885028 0.9850876 0.6913076 0.5401008
[4,] 0.3192396 1.0849529 0.9591183 0.8786824
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 225.21507 40.60639 33.90374 32.01130
[2,] 32.34475 34.89201 39.66312 35.79753
[3,] 37.06987 35.82127 32.39098 30.69272
[4,] 28.29431 37.02665 35.51109 34.55891
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x000001d23d6ff4d0>
> exp(tmp5)
<pointer: 0x000001d23d6ff4d0>
> log(tmp5,2)
<pointer: 0x000001d23d6ff4d0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 468.7557
> Min(tmp5)
[1] 54.1191
> mean(tmp5)
[1] 72.92062
> Sum(tmp5)
[1] 14584.12
> Var(tmp5)
[1] 862.3119
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 90.40912 70.00402 69.60084 72.91929 70.14388 69.04078 71.97667 72.86470
[9] 71.45411 70.79276
> rowSums(tmp5)
[1] 1808.182 1400.080 1392.017 1458.386 1402.878 1380.816 1439.533 1457.294
[9] 1429.082 1415.855
> rowVars(tmp5)
[1] 8028.15415 57.20265 64.19310 55.62842 43.51280 87.31963
[7] 97.18957 108.51508 55.02969 60.40488
> rowSd(tmp5)
[1] 89.599967 7.563243 8.012060 7.458446 6.596423 9.344497 9.858477
[8] 10.417057 7.418200 7.772057
> rowMax(tmp5)
[1] 468.75566 82.55360 83.64548 83.86895 86.63915 83.61096 100.27754
[8] 97.26418 87.36553 87.84458
> rowMin(tmp5)
[1] 55.23718 54.69538 55.95074 58.89090 61.26274 54.46289 54.11910 55.79033
[9] 58.00997 59.76629
>
> colMeans(tmp5)
[1] 106.68743 71.38929 75.63331 73.58694 73.21843 71.41416 78.56938
[8] 74.24395 69.26091 69.03001 70.85359 71.60320 66.12785 69.00595
[15] 67.78933 70.63217 73.40790 65.30736 72.00532 68.64586
> colSums(tmp5)
[1] 1066.8743 713.8929 756.3331 735.8694 732.1843 714.1416 785.6938
[8] 742.4395 692.6091 690.3001 708.5359 716.0320 661.2785 690.0595
[15] 677.8933 706.3217 734.0790 653.0736 720.0532 686.4586
> colVars(tmp5)
[1] 16232.72205 56.70263 34.53615 44.43695 97.83610 37.94809
[7] 65.86563 54.54952 60.55590 74.55882 151.56402 101.12547
[13] 81.10760 64.90752 50.61700 81.51982 97.89338 36.20418
[19] 47.44821 48.74732
> colSd(tmp5)
[1] 127.407700 7.530115 5.876747 6.666104 9.891213 6.160202
[7] 8.115764 7.385765 7.781767 8.634745 12.311134 10.056116
[13] 9.005976 8.056520 7.114562 9.028833 9.894108 6.016991
[19] 6.888266 6.981928
> colMax(tmp5)
[1] 468.75566 84.51688 86.63915 85.22693 87.84458 82.58522 97.26418
[8] 84.84116 78.83321 83.86895 100.27754 82.11889 79.44079 87.36553
[15] 78.94180 82.29846 88.50453 76.89317 81.17103 78.15848
> colMin(tmp5)
[1] 54.94897 58.00997 67.41759 63.88287 54.69538 60.46404 69.28167 64.51263
[9] 59.47512 55.02120 55.23718 54.11910 54.46289 61.01830 55.95074 57.66066
[17] 61.26274 56.59897 63.36376 56.85098
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 90.40912 70.00402 69.60084 72.91929 70.14388 69.04078 71.97667 72.86470
[9] 71.45411 NA
> rowSums(tmp5)
[1] 1808.182 1400.080 1392.017 1458.386 1402.878 1380.816 1439.533 1457.294
[9] 1429.082 NA
> rowVars(tmp5)
[1] 8028.15415 57.20265 64.19310 55.62842 43.51280 87.31963
[7] 97.18957 108.51508 55.02969 62.47681
> rowSd(tmp5)
[1] 89.599967 7.563243 8.012060 7.458446 6.596423 9.344497 9.858477
[8] 10.417057 7.418200 7.904228
> rowMax(tmp5)
[1] 468.75566 82.55360 83.64548 83.86895 86.63915 83.61096 100.27754
[8] 97.26418 87.36553 NA
> rowMin(tmp5)
[1] 55.23718 54.69538 55.95074 58.89090 61.26274 54.46289 54.11910 55.79033
[9] 58.00997 NA
>
> colMeans(tmp5)
[1] 106.68743 71.38929 75.63331 73.58694 73.21843 71.41416 78.56938
[8] NA 69.26091 69.03001 70.85359 71.60320 66.12785 69.00595
[15] 67.78933 70.63217 73.40790 65.30736 72.00532 68.64586
> colSums(tmp5)
[1] 1066.8743 713.8929 756.3331 735.8694 732.1843 714.1416 785.6938
[8] NA 692.6091 690.3001 708.5359 716.0320 661.2785 690.0595
[15] 677.8933 706.3217 734.0790 653.0736 720.0532 686.4586
> colVars(tmp5)
[1] 16232.72205 56.70263 34.53615 44.43695 97.83610 37.94809
[7] 65.86563 NA 60.55590 74.55882 151.56402 101.12547
[13] 81.10760 64.90752 50.61700 81.51982 97.89338 36.20418
[19] 47.44821 48.74732
> colSd(tmp5)
[1] 127.407700 7.530115 5.876747 6.666104 9.891213 6.160202
[7] 8.115764 NA 7.781767 8.634745 12.311134 10.056116
[13] 9.005976 8.056520 7.114562 9.028833 9.894108 6.016991
[19] 6.888266 6.981928
> colMax(tmp5)
[1] 468.75566 84.51688 86.63915 85.22693 87.84458 82.58522 97.26418
[8] NA 78.83321 83.86895 100.27754 82.11889 79.44079 87.36553
[15] 78.94180 82.29846 88.50453 76.89317 81.17103 78.15848
> colMin(tmp5)
[1] 54.94897 58.00997 67.41759 63.88287 54.69538 60.46404 69.28167 NA
[9] 59.47512 55.02120 55.23718 54.11910 54.46289 61.01830 55.95074 57.66066
[17] 61.26274 56.59897 63.36376 56.85098
>
> Max(tmp5,na.rm=TRUE)
[1] 468.7557
> Min(tmp5,na.rm=TRUE)
[1] 54.1191
> mean(tmp5,na.rm=TRUE)
[1] 72.90776
> Sum(tmp5,na.rm=TRUE)
[1] 14508.65
> Var(tmp5,na.rm=TRUE)
[1] 866.6338
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.40912 70.00402 69.60084 72.91929 70.14388 69.04078 71.97667 72.86470
[9] 71.45411 70.54615
> rowSums(tmp5,na.rm=TRUE)
[1] 1808.182 1400.080 1392.017 1458.386 1402.878 1380.816 1439.533 1457.294
[9] 1429.082 1340.377
> rowVars(tmp5,na.rm=TRUE)
[1] 8028.15415 57.20265 64.19310 55.62842 43.51280 87.31963
[7] 97.18957 108.51508 55.02969 62.47681
> rowSd(tmp5,na.rm=TRUE)
[1] 89.599967 7.563243 8.012060 7.458446 6.596423 9.344497 9.858477
[8] 10.417057 7.418200 7.904228
> rowMax(tmp5,na.rm=TRUE)
[1] 468.75566 82.55360 83.64548 83.86895 86.63915 83.61096 100.27754
[8] 97.26418 87.36553 87.84458
> rowMin(tmp5,na.rm=TRUE)
[1] 55.23718 54.69538 55.95074 58.89090 61.26274 54.46289 54.11910 55.79033
[9] 58.00997 59.76629
>
> colMeans(tmp5,na.rm=TRUE)
[1] 106.68743 71.38929 75.63331 73.58694 73.21843 71.41416 78.56938
[8] 74.10679 69.26091 69.03001 70.85359 71.60320 66.12785 69.00595
[15] 67.78933 70.63217 73.40790 65.30736 72.00532 68.64586
> colSums(tmp5,na.rm=TRUE)
[1] 1066.8743 713.8929 756.3331 735.8694 732.1843 714.1416 785.6938
[8] 666.9611 692.6091 690.3001 708.5359 716.0320 661.2785 690.0595
[15] 677.8933 706.3217 734.0790 653.0736 720.0532 686.4586
> colVars(tmp5,na.rm=TRUE)
[1] 16232.72205 56.70263 34.53615 44.43695 97.83610 37.94809
[7] 65.86563 61.15659 60.55590 74.55882 151.56402 101.12547
[13] 81.10760 64.90752 50.61700 81.51982 97.89338 36.20418
[19] 47.44821 48.74732
> colSd(tmp5,na.rm=TRUE)
[1] 127.407700 7.530115 5.876747 6.666104 9.891213 6.160202
[7] 8.115764 7.820268 7.781767 8.634745 12.311134 10.056116
[13] 9.005976 8.056520 7.114562 9.028833 9.894108 6.016991
[19] 6.888266 6.981928
> colMax(tmp5,na.rm=TRUE)
[1] 468.75566 84.51688 86.63915 85.22693 87.84458 82.58522 97.26418
[8] 84.84116 78.83321 83.86895 100.27754 82.11889 79.44079 87.36553
[15] 78.94180 82.29846 88.50453 76.89317 81.17103 78.15848
> colMin(tmp5,na.rm=TRUE)
[1] 54.94897 58.00997 67.41759 63.88287 54.69538 60.46404 69.28167 64.51263
[9] 59.47512 55.02120 55.23718 54.11910 54.46289 61.01830 55.95074 57.66066
[17] 61.26274 56.59897 63.36376 56.85098
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 90.40912 70.00402 69.60084 72.91929 70.14388 69.04078 71.97667 72.86470
[9] 71.45411 NaN
> rowSums(tmp5,na.rm=TRUE)
[1] 1808.182 1400.080 1392.017 1458.386 1402.878 1380.816 1439.533 1457.294
[9] 1429.082 0.000
> rowVars(tmp5,na.rm=TRUE)
[1] 8028.15415 57.20265 64.19310 55.62842 43.51280 87.31963
[7] 97.18957 108.51508 55.02969 NA
> rowSd(tmp5,na.rm=TRUE)
[1] 89.599967 7.563243 8.012060 7.458446 6.596423 9.344497 9.858477
[8] 10.417057 7.418200 NA
> rowMax(tmp5,na.rm=TRUE)
[1] 468.75566 82.55360 83.64548 83.86895 86.63915 83.61096 100.27754
[8] 97.26418 87.36553 NA
> rowMin(tmp5,na.rm=TRUE)
[1] 55.23718 54.69538 55.95074 58.89090 61.26274 54.46289 54.11910 55.79033
[9] 58.00997 NA
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] 111.88535 71.78943 75.35601 73.81273 71.59331 72.63084 79.17758
[8] NaN 68.48672 69.59510 72.08551 70.47678 65.96266 68.50132
[15] 68.64500 70.78186 72.83737 64.42820 72.05864 68.92971
> colSums(tmp5,na.rm=TRUE)
[1] 1006.9681 646.1049 678.2041 664.3145 644.3398 653.6776 712.5982
[8] 0.0000 616.3805 626.3559 648.7696 634.2910 593.6640 616.5119
[15] 617.8050 637.0367 655.5363 579.8538 648.5277 620.3674
> colVars(tmp5,na.rm=TRUE)
[1] 17957.85550 61.98917 37.98814 49.41803 80.35395 26.03812
[7] 69.93739 NA 61.38250 80.28626 153.43615 99.49182
[13] 90.93906 70.15616 48.70714 91.45774 106.46811 32.03435
[19] 53.34726 53.93432
> colSd(tmp5,na.rm=TRUE)
[1] 134.006923 7.873320 6.163452 7.029796 8.964036 5.102756
[7] 8.362858 NA 7.834698 8.960260 12.386935 9.974559
[13] 9.536197 8.375927 6.979050 9.563354 10.318339 5.659889
[19] 7.303921 7.343999
> colMax(tmp5,na.rm=TRUE)
[1] 468.75566 84.51688 86.63915 85.22693 83.64548 82.58522 97.26418
[8] -Inf 78.83321 83.86895 100.27754 82.11889 79.44079 87.36553
[15] 78.94180 82.29846 88.50453 76.89317 81.17103 78.15848
> colMin(tmp5,na.rm=TRUE)
[1] 54.94897 58.00997 67.41759 63.88287 54.69538 67.17499 69.28167 Inf
[9] 59.47512 55.02120 55.23718 54.11910 54.46289 61.01830 55.95074 57.66066
[17] 61.26274 56.59897 63.36376 56.85098
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 200.8928 412.4074 342.2236 314.0395 336.7268 245.6385 228.4983 226.1128
[9] 205.9356 221.0540
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 200.8928 412.4074 342.2236 314.0395 336.7268 245.6385 228.4983 226.1128
[9] 205.9356 221.0540
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] -2.842171e-14 1.136868e-13 0.000000e+00 -3.979039e-13 0.000000e+00
[6] 2.842171e-14 -1.136868e-13 -1.136868e-13 -2.842171e-14 -1.136868e-13
[11] -8.526513e-14 1.705303e-13 1.421085e-13 -9.947598e-14 2.273737e-13
[16] 1.705303e-13 5.684342e-14 4.263256e-14 -2.273737e-13 2.842171e-14
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
1 18
8 20
5 3
6 10
2 7
8 14
5 4
7 17
10 14
4 3
6 8
2 5
7 2
8 13
1 7
3 5
10 1
1 11
6 19
9 20
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 2.967668
> Min(tmp)
[1] -1.880175
> mean(tmp)
[1] 0.01354353
> Sum(tmp)
[1] 1.354353
> Var(tmp)
[1] 0.8675303
>
> rowMeans(tmp)
[1] 0.01354353
> rowSums(tmp)
[1] 1.354353
> rowVars(tmp)
[1] 0.8675303
> rowSd(tmp)
[1] 0.9314131
> rowMax(tmp)
[1] 2.967668
> rowMin(tmp)
[1] -1.880175
>
> colMeans(tmp)
[1] 0.201010935 0.267411398 -0.524034676 0.319129422 -0.092085663
[6] 0.395086052 -0.234685848 1.317599056 -1.830152406 -1.525211026
[11] 0.400522367 -0.496202059 0.100038751 -0.578979760 -1.117263045
[16] -1.777072653 -0.039493033 -0.682259890 0.002998240 0.126326897
[21] -0.323549451 0.236102249 0.575989045 0.477140816 0.178189978
[26] 0.550256406 0.704181765 -1.297690893 2.619758681 0.666237197
[31] -0.617821147 1.416379284 1.133925612 0.050448315 -0.439129713
[36] 0.482165936 0.021079888 1.916905240 0.879835339 -1.045738053
[41] -1.056186625 0.986672151 0.822372621 0.254458117 2.967667569
[46] -0.389711577 -0.816782126 -1.248538817 -0.910217594 -1.488991263
[51] -1.058501911 0.547441732 0.486642434 -0.661589393 -0.096258323
[56] 0.557926424 -0.174193778 -0.305735394 -0.848328603 -1.880174631
[61] -0.198628046 -0.218230243 0.329259787 0.707230780 -0.642351152
[66] -0.875919653 0.126683641 -0.184171807 -0.521515217 -0.988188970
[71] 0.015940726 1.316098463 1.798555592 -1.869826304 0.390255625
[76] -0.645253745 0.699154728 0.009629475 -0.811424068 -1.298766865
[81] -0.319101512 -0.041656131 1.169332372 1.163460328 0.041495088
[86] 0.289181031 0.641791502 1.214535955 0.952243683 0.459565511
[91] -0.149721488 0.756613551 0.229907015 -0.398668518 -0.156245322
[96] -0.667875474 1.565769341 1.238437602 -0.693156683 -1.185407684
> colSums(tmp)
[1] 0.201010935 0.267411398 -0.524034676 0.319129422 -0.092085663
[6] 0.395086052 -0.234685848 1.317599056 -1.830152406 -1.525211026
[11] 0.400522367 -0.496202059 0.100038751 -0.578979760 -1.117263045
[16] -1.777072653 -0.039493033 -0.682259890 0.002998240 0.126326897
[21] -0.323549451 0.236102249 0.575989045 0.477140816 0.178189978
[26] 0.550256406 0.704181765 -1.297690893 2.619758681 0.666237197
[31] -0.617821147 1.416379284 1.133925612 0.050448315 -0.439129713
[36] 0.482165936 0.021079888 1.916905240 0.879835339 -1.045738053
[41] -1.056186625 0.986672151 0.822372621 0.254458117 2.967667569
[46] -0.389711577 -0.816782126 -1.248538817 -0.910217594 -1.488991263
[51] -1.058501911 0.547441732 0.486642434 -0.661589393 -0.096258323
[56] 0.557926424 -0.174193778 -0.305735394 -0.848328603 -1.880174631
[61] -0.198628046 -0.218230243 0.329259787 0.707230780 -0.642351152
[66] -0.875919653 0.126683641 -0.184171807 -0.521515217 -0.988188970
[71] 0.015940726 1.316098463 1.798555592 -1.869826304 0.390255625
[76] -0.645253745 0.699154728 0.009629475 -0.811424068 -1.298766865
[81] -0.319101512 -0.041656131 1.169332372 1.163460328 0.041495088
[86] 0.289181031 0.641791502 1.214535955 0.952243683 0.459565511
[91] -0.149721488 0.756613551 0.229907015 -0.398668518 -0.156245322
[96] -0.667875474 1.565769341 1.238437602 -0.693156683 -1.185407684
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] 0.201010935 0.267411398 -0.524034676 0.319129422 -0.092085663
[6] 0.395086052 -0.234685848 1.317599056 -1.830152406 -1.525211026
[11] 0.400522367 -0.496202059 0.100038751 -0.578979760 -1.117263045
[16] -1.777072653 -0.039493033 -0.682259890 0.002998240 0.126326897
[21] -0.323549451 0.236102249 0.575989045 0.477140816 0.178189978
[26] 0.550256406 0.704181765 -1.297690893 2.619758681 0.666237197
[31] -0.617821147 1.416379284 1.133925612 0.050448315 -0.439129713
[36] 0.482165936 0.021079888 1.916905240 0.879835339 -1.045738053
[41] -1.056186625 0.986672151 0.822372621 0.254458117 2.967667569
[46] -0.389711577 -0.816782126 -1.248538817 -0.910217594 -1.488991263
[51] -1.058501911 0.547441732 0.486642434 -0.661589393 -0.096258323
[56] 0.557926424 -0.174193778 -0.305735394 -0.848328603 -1.880174631
[61] -0.198628046 -0.218230243 0.329259787 0.707230780 -0.642351152
[66] -0.875919653 0.126683641 -0.184171807 -0.521515217 -0.988188970
[71] 0.015940726 1.316098463 1.798555592 -1.869826304 0.390255625
[76] -0.645253745 0.699154728 0.009629475 -0.811424068 -1.298766865
[81] -0.319101512 -0.041656131 1.169332372 1.163460328 0.041495088
[86] 0.289181031 0.641791502 1.214535955 0.952243683 0.459565511
[91] -0.149721488 0.756613551 0.229907015 -0.398668518 -0.156245322
[96] -0.667875474 1.565769341 1.238437602 -0.693156683 -1.185407684
> colMin(tmp)
[1] 0.201010935 0.267411398 -0.524034676 0.319129422 -0.092085663
[6] 0.395086052 -0.234685848 1.317599056 -1.830152406 -1.525211026
[11] 0.400522367 -0.496202059 0.100038751 -0.578979760 -1.117263045
[16] -1.777072653 -0.039493033 -0.682259890 0.002998240 0.126326897
[21] -0.323549451 0.236102249 0.575989045 0.477140816 0.178189978
[26] 0.550256406 0.704181765 -1.297690893 2.619758681 0.666237197
[31] -0.617821147 1.416379284 1.133925612 0.050448315 -0.439129713
[36] 0.482165936 0.021079888 1.916905240 0.879835339 -1.045738053
[41] -1.056186625 0.986672151 0.822372621 0.254458117 2.967667569
[46] -0.389711577 -0.816782126 -1.248538817 -0.910217594 -1.488991263
[51] -1.058501911 0.547441732 0.486642434 -0.661589393 -0.096258323
[56] 0.557926424 -0.174193778 -0.305735394 -0.848328603 -1.880174631
[61] -0.198628046 -0.218230243 0.329259787 0.707230780 -0.642351152
[66] -0.875919653 0.126683641 -0.184171807 -0.521515217 -0.988188970
[71] 0.015940726 1.316098463 1.798555592 -1.869826304 0.390255625
[76] -0.645253745 0.699154728 0.009629475 -0.811424068 -1.298766865
[81] -0.319101512 -0.041656131 1.169332372 1.163460328 0.041495088
[86] 0.289181031 0.641791502 1.214535955 0.952243683 0.459565511
[91] -0.149721488 0.756613551 0.229907015 -0.398668518 -0.156245322
[96] -0.667875474 1.565769341 1.238437602 -0.693156683 -1.185407684
> colMedians(tmp)
[1] 0.201010935 0.267411398 -0.524034676 0.319129422 -0.092085663
[6] 0.395086052 -0.234685848 1.317599056 -1.830152406 -1.525211026
[11] 0.400522367 -0.496202059 0.100038751 -0.578979760 -1.117263045
[16] -1.777072653 -0.039493033 -0.682259890 0.002998240 0.126326897
[21] -0.323549451 0.236102249 0.575989045 0.477140816 0.178189978
[26] 0.550256406 0.704181765 -1.297690893 2.619758681 0.666237197
[31] -0.617821147 1.416379284 1.133925612 0.050448315 -0.439129713
[36] 0.482165936 0.021079888 1.916905240 0.879835339 -1.045738053
[41] -1.056186625 0.986672151 0.822372621 0.254458117 2.967667569
[46] -0.389711577 -0.816782126 -1.248538817 -0.910217594 -1.488991263
[51] -1.058501911 0.547441732 0.486642434 -0.661589393 -0.096258323
[56] 0.557926424 -0.174193778 -0.305735394 -0.848328603 -1.880174631
[61] -0.198628046 -0.218230243 0.329259787 0.707230780 -0.642351152
[66] -0.875919653 0.126683641 -0.184171807 -0.521515217 -0.988188970
[71] 0.015940726 1.316098463 1.798555592 -1.869826304 0.390255625
[76] -0.645253745 0.699154728 0.009629475 -0.811424068 -1.298766865
[81] -0.319101512 -0.041656131 1.169332372 1.163460328 0.041495088
[86] 0.289181031 0.641791502 1.214535955 0.952243683 0.459565511
[91] -0.149721488 0.756613551 0.229907015 -0.398668518 -0.156245322
[96] -0.667875474 1.565769341 1.238437602 -0.693156683 -1.185407684
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.2010109 0.2674114 -0.5240347 0.3191294 -0.09208566 0.3950861 -0.2346858
[2,] 0.2010109 0.2674114 -0.5240347 0.3191294 -0.09208566 0.3950861 -0.2346858
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] 1.317599 -1.830152 -1.525211 0.4005224 -0.4962021 0.1000388 -0.5789798
[2,] 1.317599 -1.830152 -1.525211 0.4005224 -0.4962021 0.1000388 -0.5789798
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -1.117263 -1.777073 -0.03949303 -0.6822599 0.00299824 0.1263269 -0.3235495
[2,] -1.117263 -1.777073 -0.03949303 -0.6822599 0.00299824 0.1263269 -0.3235495
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] 0.2361022 0.575989 0.4771408 0.17819 0.5502564 0.7041818 -1.297691
[2,] 0.2361022 0.575989 0.4771408 0.17819 0.5502564 0.7041818 -1.297691
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] 2.619759 0.6662372 -0.6178211 1.416379 1.133926 0.05044832 -0.4391297
[2,] 2.619759 0.6662372 -0.6178211 1.416379 1.133926 0.05044832 -0.4391297
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] 0.4821659 0.02107989 1.916905 0.8798353 -1.045738 -1.056187 0.9866722
[2,] 0.4821659 0.02107989 1.916905 0.8798353 -1.045738 -1.056187 0.9866722
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] 0.8223726 0.2544581 2.967668 -0.3897116 -0.8167821 -1.248539 -0.9102176
[2,] 0.8223726 0.2544581 2.967668 -0.3897116 -0.8167821 -1.248539 -0.9102176
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] -1.488991 -1.058502 0.5474417 0.4866424 -0.6615894 -0.09625832 0.5579264
[2,] -1.488991 -1.058502 0.5474417 0.4866424 -0.6615894 -0.09625832 0.5579264
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] -0.1741938 -0.3057354 -0.8483286 -1.880175 -0.198628 -0.2182302 0.3292598
[2,] -0.1741938 -0.3057354 -0.8483286 -1.880175 -0.198628 -0.2182302 0.3292598
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] 0.7072308 -0.6423512 -0.8759197 0.1266836 -0.1841718 -0.5215152 -0.988189
[2,] 0.7072308 -0.6423512 -0.8759197 0.1266836 -0.1841718 -0.5215152 -0.988189
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.01594073 1.316098 1.798556 -1.869826 0.3902556 -0.6452537 0.6991547
[2,] 0.01594073 1.316098 1.798556 -1.869826 0.3902556 -0.6452537 0.6991547
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.009629475 -0.8114241 -1.298767 -0.3191015 -0.04165613 1.169332 1.16346
[2,] 0.009629475 -0.8114241 -1.298767 -0.3191015 -0.04165613 1.169332 1.16346
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] 0.04149509 0.289181 0.6417915 1.214536 0.9522437 0.4595655 -0.1497215
[2,] 0.04149509 0.289181 0.6417915 1.214536 0.9522437 0.4595655 -0.1497215
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] 0.7566136 0.229907 -0.3986685 -0.1562453 -0.6678755 1.565769 1.238438
[2,] 0.7566136 0.229907 -0.3986685 -0.1562453 -0.6678755 1.565769 1.238438
[,99] [,100]
[1,] -0.6931567 -1.185408
[2,] -0.6931567 -1.185408
>
>
> Max(tmp2)
[1] 3.112976
> Min(tmp2)
[1] -2.801919
> mean(tmp2)
[1] -0.04182181
> Sum(tmp2)
[1] -4.182181
> Var(tmp2)
[1] 1.065246
>
> rowMeans(tmp2)
[1] 2.20179979 0.59781824 0.48363245 1.68589531 -0.49091229 -1.21420768
[7] -0.40276217 -1.04407523 -0.35104407 -0.47703086 0.04818909 -0.36069213
[13] -1.58339390 0.12447618 -0.84390513 -0.11882746 -0.40342063 -0.02124200
[19] 0.24379760 0.73879614 0.67369253 1.47112002 0.69831528 -0.74138891
[25] 0.04839442 -0.73727971 -1.00086851 -0.17650250 0.17041409 -0.26543464
[31] -0.43238662 -0.15015709 -0.86234552 0.78751418 -0.37685775 -0.51369475
[37] 0.84813293 -0.12497260 0.29227057 -0.19571583 1.99731219 0.08172164
[43] -1.13102180 0.21255589 0.86725177 -0.57221997 0.27990161 -1.24726391
[49] -2.55745904 0.52984290 -0.45148014 -1.94560635 0.44900898 -0.76498045
[55] 0.01379537 1.81501227 -0.59874692 -0.68035100 0.41049578 -0.96831537
[61] -0.17546213 -0.56397881 -0.74180985 -0.32234545 0.79216763 0.75195170
[67] -1.46957299 1.02526299 0.71138381 0.46175133 -1.66965670 -0.46344184
[73] -1.79024857 3.11297598 -0.13597613 0.70418277 -1.17816010 -0.54966909
[79] -0.22428582 -0.32794091 0.29134945 -0.93352235 0.66253891 0.52211275
[85] 0.24801631 -0.33293686 0.62126566 1.81737797 -1.53712918 -1.25832300
[91] 0.12228599 2.54938727 -0.68292830 0.67174852 0.92206286 0.74230816
[97] -0.93130152 1.23090057 -2.80191922 1.98280259
> rowSums(tmp2)
[1] 2.20179979 0.59781824 0.48363245 1.68589531 -0.49091229 -1.21420768
[7] -0.40276217 -1.04407523 -0.35104407 -0.47703086 0.04818909 -0.36069213
[13] -1.58339390 0.12447618 -0.84390513 -0.11882746 -0.40342063 -0.02124200
[19] 0.24379760 0.73879614 0.67369253 1.47112002 0.69831528 -0.74138891
[25] 0.04839442 -0.73727971 -1.00086851 -0.17650250 0.17041409 -0.26543464
[31] -0.43238662 -0.15015709 -0.86234552 0.78751418 -0.37685775 -0.51369475
[37] 0.84813293 -0.12497260 0.29227057 -0.19571583 1.99731219 0.08172164
[43] -1.13102180 0.21255589 0.86725177 -0.57221997 0.27990161 -1.24726391
[49] -2.55745904 0.52984290 -0.45148014 -1.94560635 0.44900898 -0.76498045
[55] 0.01379537 1.81501227 -0.59874692 -0.68035100 0.41049578 -0.96831537
[61] -0.17546213 -0.56397881 -0.74180985 -0.32234545 0.79216763 0.75195170
[67] -1.46957299 1.02526299 0.71138381 0.46175133 -1.66965670 -0.46344184
[73] -1.79024857 3.11297598 -0.13597613 0.70418277 -1.17816010 -0.54966909
[79] -0.22428582 -0.32794091 0.29134945 -0.93352235 0.66253891 0.52211275
[85] 0.24801631 -0.33293686 0.62126566 1.81737797 -1.53712918 -1.25832300
[91] 0.12228599 2.54938727 -0.68292830 0.67174852 0.92206286 0.74230816
[97] -0.93130152 1.23090057 -2.80191922 1.98280259
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] 2.20179979 0.59781824 0.48363245 1.68589531 -0.49091229 -1.21420768
[7] -0.40276217 -1.04407523 -0.35104407 -0.47703086 0.04818909 -0.36069213
[13] -1.58339390 0.12447618 -0.84390513 -0.11882746 -0.40342063 -0.02124200
[19] 0.24379760 0.73879614 0.67369253 1.47112002 0.69831528 -0.74138891
[25] 0.04839442 -0.73727971 -1.00086851 -0.17650250 0.17041409 -0.26543464
[31] -0.43238662 -0.15015709 -0.86234552 0.78751418 -0.37685775 -0.51369475
[37] 0.84813293 -0.12497260 0.29227057 -0.19571583 1.99731219 0.08172164
[43] -1.13102180 0.21255589 0.86725177 -0.57221997 0.27990161 -1.24726391
[49] -2.55745904 0.52984290 -0.45148014 -1.94560635 0.44900898 -0.76498045
[55] 0.01379537 1.81501227 -0.59874692 -0.68035100 0.41049578 -0.96831537
[61] -0.17546213 -0.56397881 -0.74180985 -0.32234545 0.79216763 0.75195170
[67] -1.46957299 1.02526299 0.71138381 0.46175133 -1.66965670 -0.46344184
[73] -1.79024857 3.11297598 -0.13597613 0.70418277 -1.17816010 -0.54966909
[79] -0.22428582 -0.32794091 0.29134945 -0.93352235 0.66253891 0.52211275
[85] 0.24801631 -0.33293686 0.62126566 1.81737797 -1.53712918 -1.25832300
[91] 0.12228599 2.54938727 -0.68292830 0.67174852 0.92206286 0.74230816
[97] -0.93130152 1.23090057 -2.80191922 1.98280259
> rowMin(tmp2)
[1] 2.20179979 0.59781824 0.48363245 1.68589531 -0.49091229 -1.21420768
[7] -0.40276217 -1.04407523 -0.35104407 -0.47703086 0.04818909 -0.36069213
[13] -1.58339390 0.12447618 -0.84390513 -0.11882746 -0.40342063 -0.02124200
[19] 0.24379760 0.73879614 0.67369253 1.47112002 0.69831528 -0.74138891
[25] 0.04839442 -0.73727971 -1.00086851 -0.17650250 0.17041409 -0.26543464
[31] -0.43238662 -0.15015709 -0.86234552 0.78751418 -0.37685775 -0.51369475
[37] 0.84813293 -0.12497260 0.29227057 -0.19571583 1.99731219 0.08172164
[43] -1.13102180 0.21255589 0.86725177 -0.57221997 0.27990161 -1.24726391
[49] -2.55745904 0.52984290 -0.45148014 -1.94560635 0.44900898 -0.76498045
[55] 0.01379537 1.81501227 -0.59874692 -0.68035100 0.41049578 -0.96831537
[61] -0.17546213 -0.56397881 -0.74180985 -0.32234545 0.79216763 0.75195170
[67] -1.46957299 1.02526299 0.71138381 0.46175133 -1.66965670 -0.46344184
[73] -1.79024857 3.11297598 -0.13597613 0.70418277 -1.17816010 -0.54966909
[79] -0.22428582 -0.32794091 0.29134945 -0.93352235 0.66253891 0.52211275
[85] 0.24801631 -0.33293686 0.62126566 1.81737797 -1.53712918 -1.25832300
[91] 0.12228599 2.54938727 -0.68292830 0.67174852 0.92206286 0.74230816
[97] -0.93130152 1.23090057 -2.80191922 1.98280259
>
> colMeans(tmp2)
[1] -0.04182181
> colSums(tmp2)
[1] -4.182181
> colVars(tmp2)
[1] 1.065246
> colSd(tmp2)
[1] 1.032107
> colMax(tmp2)
[1] 3.112976
> colMin(tmp2)
[1] -2.801919
> colMedians(tmp2)
[1] -0.1430666
> colRanges(tmp2)
[,1]
[1,] -2.801919
[2,] 3.112976
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] -0.9805494 0.4353658 7.6865210 -0.3829532 2.6911583 -1.9315042
[7] -1.9173107 1.7064543 -2.1263243 1.7778978
> colApply(tmp,quantile)[,1]
[,1]
[1,] -2.40475469
[2,] -0.77264484
[3,] 0.08039998
[4,] 0.58766789
[5,] 1.75134267
>
> rowApply(tmp,sum)
[1] -1.54788732 -2.41030913 -0.06026317 1.99049770 4.20782801 -3.35282091
[7] 0.19925865 4.11379261 0.39633850 3.42232059
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 2 6 8 3 4 3 6 10 1 8
[2,] 10 2 2 9 5 1 9 2 10 1
[3,] 7 10 9 10 10 9 5 8 8 3
[4,] 5 9 3 4 1 6 2 4 9 9
[5,] 9 4 5 1 3 10 7 9 7 4
[6,] 4 1 1 5 7 7 10 5 3 5
[7,] 1 8 6 8 9 2 1 1 6 7
[8,] 6 3 10 7 6 4 8 6 4 6
[9,] 3 7 4 2 8 8 3 3 5 2
[10,] 8 5 7 6 2 5 4 7 2 10
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -1.78371004 0.72565429 -0.84304232 -0.48988888 -4.02085042 -1.88376608
[7] 4.52259848 -0.88859405 -0.04422513 0.85385639 -1.18750857 -1.85527489
[13] -0.22763695 -3.32631905 0.21068261 -0.09422975 -1.94460726 -3.41244083
[19] -4.48210704 -1.48012632
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.18247301
[2,] -0.28323713
[3,] -0.28309335
[4,] -0.08022969
[5,] 0.04532313
>
> rowApply(tmp,sum)
[1] -8.917645 -3.785079 -5.319884 -6.777322 3.148394
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 4 13 12 8 8
[2,] 17 19 17 13 3
[3,] 6 9 10 16 11
[4,] 10 12 18 9 6
[5,] 13 11 1 2 16
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -1.18247301 0.16331983 -1.0472355 -0.7420996 -0.2515472 -0.3856365
[2,] 0.04532313 1.12497816 -0.2118368 -0.0195202 -0.1563479 0.1791392
[3,] -0.28309335 0.71138260 -0.4547251 0.8223029 -2.4412939 -0.3104906
[4,] -0.28323713 -0.02942797 0.7374585 -0.2507608 -2.3536552 -2.0238088
[5,] -0.08022969 -1.24459833 0.1332966 -0.2998111 1.1819938 0.6570306
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 1.055937 -0.03871290 0.08921719 -0.7371211 -0.84877319 -1.4259439
[2,] -0.276561 -1.06954867 0.63224446 2.2688121 0.09226225 0.1537140
[3,] 1.234174 2.08722999 -1.56822092 -0.7405212 -0.75665521 -0.2511566
[4,] 1.248913 -0.08947919 1.40871033 -1.1448677 -0.18810514 -0.1445704
[5,] 1.260136 -1.77808328 -0.60617618 1.2075542 0.51376272 -0.1873181
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] -0.9000239 -1.3013156 -1.0726285 1.10890215 -1.4189965 0.064046038
[2,] 0.5576970 -1.0595225 -0.6244596 -1.48157227 -0.7633704 -1.961876628
[3,] -0.2829734 -0.5021709 -0.9765073 0.27208069 -0.8093389 -0.567811790
[4,] -1.1146670 1.0721995 1.7226172 0.04929757 0.6055251 -0.945132359
[5,] 1.5123303 -1.5355095 1.1616608 -0.04293789 0.4415734 -0.001666095
[,19] [,20]
[1,] -0.7655592 0.7189996
[2,] -0.1755984 -1.0390348
[3,] 0.1321132 -0.6342082
[4,] -2.8649049 -2.1894265
[5,] -0.8081577 1.6635436
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.8 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 625 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 541 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.8 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 0.1496145 1.029281 0.3216949 0.218197 2.374122 0.2006049 -2.172151
col8 col9 col10 col11 col12 col13 col14
row1 0.4944888 -1.583619 -1.078555 1.124241 0.7629744 -0.06456712 1.277911
col15 col16 col17 col18 col19 col20
row1 -0.6072915 -0.5924559 -0.6363366 1.857558 1.742723 -0.5378218
> tmp[,"col10"]
col10
row1 -1.0785553
row2 -0.2405146
row3 0.9108251
row4 -0.6423363
row5 0.4728519
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 0.1496145 1.02928094 0.3216949 0.2181970 2.374122 0.2006049 -2.1721512
row5 -0.3346903 -0.06624449 0.3060129 0.3930427 1.017316 -0.4588076 -0.3959901
col8 col9 col10 col11 col12 col13
row1 0.4944888 -1.583619 -1.0785553 1.124241 0.7629744 -0.06456712
row5 0.4085723 1.002164 0.4728519 -1.227800 -0.5966612 -0.58870350
col14 col15 col16 col17 col18 col19
row1 1.27791069 -0.6072915 -0.5924559 -0.63633658 1.8575581 1.7427230
row5 -0.09600222 -1.3094098 -0.3761264 0.06643017 0.7112496 -0.1165628
col20
row1 -0.5378218
row5 0.6078347
> tmp[,c("col6","col20")]
col6 col20
row1 0.2006049 -0.5378218
row2 0.6391375 -1.0838558
row3 -0.1550318 -0.1535668
row4 -0.3847510 0.9210371
row5 -0.4588076 0.6078347
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 0.2006049 -0.5378218
row5 -0.4588076 0.6078347
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.96657 50.15792 49.55109 50.16242 51.04503 105.7308 49.89277 49.77956
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.3235 51.54323 51.37521 50.91943 50.35116 48.86473 51.10933 50.22962
col17 col18 col19 col20
row1 49.38842 49.26667 50.15636 105.3817
> tmp[,"col10"]
col10
row1 51.54323
row2 31.10677
row3 28.96854
row4 28.16448
row5 48.99213
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.96657 50.15792 49.55109 50.16242 51.04503 105.7308 49.89277 49.77956
row5 49.63913 50.10073 49.38636 51.37124 49.51380 104.2074 49.24194 51.40941
col9 col10 col11 col12 col13 col14 col15 col16
row1 51.32350 51.54323 51.37521 50.91943 50.35116 48.86473 51.10933 50.22962
row5 49.38989 48.99213 51.11032 51.29785 49.60006 49.63678 51.11207 50.47554
col17 col18 col19 col20
row1 49.38842 49.26667 50.15636 105.3817
row5 48.34404 50.25956 49.40351 103.9040
> tmp[,c("col6","col20")]
col6 col20
row1 105.73078 105.38166
row2 75.84100 74.82188
row3 75.80440 73.98570
row4 76.89119 73.40104
row5 104.20741 103.90397
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.7308 105.3817
row5 104.2074 103.9040
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.7308 105.3817
row5 104.2074 103.9040
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -1.5765550
[2,] 0.8127357
[3,] -0.5412797
[4,] -0.2613019
[5,] -0.6675983
> tmp[,c("col17","col7")]
col17 col7
[1,] -0.36810197 0.5034628
[2,] -1.77902877 1.6863377
[3,] -1.28735514 0.1320823
[4,] 0.02064328 0.7396808
[5,] 1.64632814 0.1146010
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] -0.5087269 0.001683495
[2,] 0.1501184 -1.236607198
[3,] -0.4428585 -1.173789766
[4,] 0.6405833 -1.379345509
[5,] 0.2528411 -0.974872118
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] -0.5087269
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] -0.5087269
[2,] 0.1501184
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row3 -1.630552 -0.1281606 -0.1099228 -1.715138 0.1816991 0.3272493 0.2611674
row1 1.568788 -0.5891923 0.7832159 -1.328117 -0.1672002 0.1016309 0.1458440
[,8] [,9] [,10] [,11] [,12] [,13]
row3 0.7936203 1.40007493 -0.193199 0.7091259 0.4830611 -1.033595
row1 -0.6415585 -0.06715261 1.761571 -0.8250440 -0.2697986 1.581393
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
row3 0.38928523 -0.3189055 0.226018 -0.2793789 -0.2905949 0.3888795 1.305105
row1 0.02866406 0.2936973 0.668718 0.2101376 2.2671581 -1.0329236 0.249102
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 1.56213 -1.107036 1.791967 0.605019 0.4295307 0.3933665 0.5685645
[,8] [,9] [,10]
row2 -1.945188 0.2750221 -0.5631887
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 1.093281 0.6441113 -1.551872 -0.3785434 -1.794466 0.8684151 -1.143244
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 2.300471 0.4728379 -0.896909 0.1213821 -0.1695352 -0.9479821 1.867354
[,15] [,16] [,17] [,18] [,19] [,20]
row5 0.5909493 1.233422 1.457519 0.5507602 -0.419031 1.190592
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x000001d23d6ffcb0>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac779add5"
[2] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac12402f59"
[3] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac19ec11cb"
[4] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac4bd91f61"
[5] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac2ba1e85"
[6] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac3a5d36fb"
[7] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac7a02d5e"
[8] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac738e3f74"
[9] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac725621"
[10] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac64dc4808"
[11] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac7758781b"
[12] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac3e2c759d"
[13] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac4a4a5374"
[14] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac79d97ab2"
[15] "F:/biocbuild/bbs-3.19-bioc/meat/BufferedMatrix.Rcheck/tests\\BM60ac2eff74bf"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x000001d2403ffb90>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x000001d2403ffb90>
Warning message:
In dir.create(new.directory) :
'F:\biocbuild\bbs-3.19-bioc\meat\BufferedMatrix.Rcheck\tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x000001d2403ffb90>
> rowMedians(tmp)
[1] 0.515245462 0.210621687 -0.298887993 -0.200707814 0.126809025
[6] -0.375414595 0.595648062 0.244191949 0.282829381 0.763303059
[11] -0.167233612 0.119854024 -0.022991928 -0.057961777 0.055721104
[16] 0.048021315 0.219816974 -0.027944328 0.082056565 -0.111460693
[21] -0.112507861 -0.007373959 -0.460833707 -0.566789694 -0.408231849
[26] 0.672456515 0.346193889 -0.160138357 0.020130509 0.009723136
[31] -0.113632266 -0.031390374 0.143166731 -0.193371545 0.132600177
[36] -0.173167511 0.080601366 -0.053054194 -0.005529931 0.042438283
[41] -0.431126963 -0.347218485 0.403395901 0.589759713 0.328220973
[46] 0.165269244 -0.492379631 0.306027750 0.120130220 0.148058024
[51] -0.871204928 -0.202944060 0.234277135 0.271412409 0.333054111
[56] -0.373932313 0.116883773 -0.206036879 0.159421532 0.065372945
[61] 0.019952307 -0.298901637 0.134217430 0.065335075 -0.653333030
[66] 0.692564058 -0.183812516 0.061117621 -0.313198971 0.248246819
[71] -0.342859703 0.542543159 0.299990416 -0.092896862 0.058179430
[76] 0.191295148 0.190991200 -0.059975540 -0.104544859 0.531712439
[81] 0.199586545 -0.190258788 0.085541341 -0.085100443 -0.010219371
[86] -0.127029284 0.310545361 0.945812327 0.327460778 -0.265322062
[91] 0.205338696 -0.446189542 0.105908573 -0.091472976 -0.149040323
[96] -0.351565261 0.140633904 0.164299146 -0.203445793 -0.329969964
[101] 0.257568799 -0.381475209 0.430769295 0.376031662 -0.267116514
[106] 0.277066030 0.171460641 0.152174583 0.005686763 -0.520216253
[111] -0.284308336 0.028404225 -0.379460820 0.220975699 -0.416524925
[116] 0.060090098 -0.438004113 0.132068219 0.250215441 0.210141418
[121] 0.291640727 -0.022776930 -0.717772122 0.105956082 -0.159378621
[126] -0.059611652 0.263345950 -0.028363430 0.540006172 -0.369742262
[131] 0.345184157 -0.220254676 0.463688789 0.163984726 -0.515189175
[136] 0.051387067 0.296447036 0.332642539 -0.048011394 -0.255244472
[141] -0.064677089 0.005987792 0.051476068 0.029793570 -0.459304961
[146] 0.007086811 0.431411700 -0.056520409 -0.130895111 -0.094132805
[151] 0.514274174 0.478063381 0.393487897 -0.299921109 -0.405486378
[156] 0.754380291 -0.406907969 0.581411335 0.312636699 -0.202620825
[161] -0.623671238 -0.162596852 -0.223910616 -0.132038468 0.437292049
[166] 0.209213618 0.614885135 0.098071594 -0.225916737 -0.078871600
[171] -0.385946032 -0.238202591 0.241806176 -0.076156613 0.148910271
[176] 0.079325254 -0.350583373 0.132872274 -0.255865815 -0.394931072
[181] -0.279508083 -0.010556785 -0.314816101 0.042147852 -0.340661875
[186] 0.288446736 -0.404181577 -0.130597341 -0.213848165 0.193433915
[191] 0.177368280 -0.556495739 0.241994471 0.106254254 0.244579135
[196] -0.197292656 0.542925152 -0.255404694 -0.265690828 -0.199222211
[201] -0.029969637 0.182753675 0.601992135 0.396015014 -0.452521897
[206] 0.029441004 -0.208311932 -0.250152714 -0.419130511 0.165842149
[211] 0.244431521 0.058571249 -0.104608426 0.013755378 -0.118372723
[216] -0.257484852 -0.404612953 0.318215881 -0.435590025 -0.330542822
[221] -0.084297041 -0.029154002 -0.097246006 0.664191444 -0.247192405
[226] 0.258511377 -0.117323915 0.070668579 -0.062495868 -0.026200258
>
> proc.time()
user system elapsed
3.59 15.90 35.17
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x000001bbd44fd830>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x000001bbd44fd830>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x000001bbd44fd830>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x000001bbd44fd830>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x000001bbd44fd950>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000001bbd44fd950>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x000001bbd44fd950>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000001bbd44fd950>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x000001bbd44fd950>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x000001bbd44fdb90>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000001bbd44fdb90>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x000001bbd44fdb90>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x000001bbd44fdb90>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x000001bbd44fdb90>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x000001bbd44fdb90>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x000001bbd44fdb90>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x000001bbd44fdb90>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x000001bbd44fdb90>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x000001bbd44fd170>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x000001bbd44fd170>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000001bbd44fd170>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000001bbd44fd170>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile521874a8219d" "BufferedMatrixFile5218c14643"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile521874a8219d" "BufferedMatrixFile5218c14643"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x000001bbd44fd290>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000001bbd44fd290>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x000001bbd44fd290>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x000001bbd44fd290>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x000001bbd44fd290>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x000001bbd44fd290>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x000001bbd44fd770>
> .Call("R_bm_AddColumn",P)
<pointer: 0x000001bbd44fd770>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x000001bbd44fd770>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x000001bbd44fd770>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x000001bbd387ab30>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x000001bbd387ab30>
> rm(P)
>
> proc.time()
user system elapsed
0.35 0.18 2.04
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.32 0.09 0.39