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BioC 3.5: CHECK report for SANTA on oaxaca

This page was generated on 2017-03-04 16:45:14 -0500 (Sat, 04 Mar 2017).

Package 1140/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SANTA 2.13.0
Alex J. Cornish
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SANTA
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: SANTA
Version: 2.13.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SANTA_2.13.0.tar.gz
StartedAt: 2017-03-04 08:44:07 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 08:45:19 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 71.3 seconds
RetCode: 0
Status:  OK 
CheckDir: SANTA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SANTA_2.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SANTA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SANTA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SANTA’ version ‘2.13.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘SANTA’ can be installed ... OK
* 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 R 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 loading without being on the library search path ... 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 ... NOTE
Compactness: no visible global function definition for ‘pnorm’
Compactness: no visible global function definition for ‘sd’
Knet : <anonymous>: no visible global function definition for
  ‘quantile’
Knet: no visible global function definition for ‘pnorm’
Knet: no visible global function definition for ‘sd’
Knode: no visible global function definition for ‘runif’
plot.Knet: no visible global function definition for ‘plot’
plot.Knet: no visible global function definition for ‘par’
plot.Knet: no visible global function definition for ‘polygon’
plot.Knet: no visible global function definition for ‘lines’
plot.Knet: no visible global function definition for ‘hist’
plot.Knet: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline hist lines par plot pnorm polygon quantile runif sd
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "plot",
             "polygon")
  importFrom("stats", "pnorm", "quantile", "runif", "sd")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/SANTA.Rcheck/00check.log’
for details.


SANTA.Rcheck/00install.out:

* installing *source* package ‘SANTA’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c computenetK_fewzeros.c -o computenetK_fewzeros.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c computenetK_manyzeros.c -o computenetK_manyzeros.o
computenetK_manyzeros.c:29:24: warning: incompatible pointer types assigning to 'int *' from 'char *' [-Wincompatible-pointer-types]
    p_which_vw_nonzero = R_alloc(n_nonzero_vertices, sizeof(int));
                       ^ ˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
1 warning generated.
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c computenodeAUK.c -o computenodeAUK.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG   -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -fPIC  -Wall -mtune=core2 -g -O2  -c computeweights.c -o computeweights.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SANTA.so computenetK_fewzeros.o computenetK_manyzeros.o computenodeAUK.o computeweights.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.5-bioc/meat/SANTA.Rcheck/SANTA/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SANTA)

SANTA.Rcheck/SANTA-Ex.timings:

nameusersystemelapsed
BinGraph1.3220.0311.353
CreateGrid0.0960.0010.097
DistGraph0.2310.0020.238
GraphDiffusion0.0170.0000.021
GraphMFPT0.0520.0010.053
Knet0.2850.0040.290
Knode0.0340.0010.034
SANTA.data0.0270.0040.031
SpreadHits0.0590.0010.059
plot.Knet0.0600.0040.064