| Back to Multiple platform build/check report for BioC 3.11 (small subset of software packages ONLY) |
This page was generated on 2020-01-24 03:57:03 -0500 (Fri, 24 Jan 2020).
| Package 1/41 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | |||||
| affy 1.65.1 Rafael A. Irizarry
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | [ WARNINGS ] | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK |
| Package: affy |
| Version: 1.65.1 |
| Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings affy_1.65.1.tar.gz |
| StartedAt: 2020-01-24 02:59:50 -0500 (Fri, 24 Jan 2020) |
| EndedAt: 2020-01-24 03:02:35 -0500 (Fri, 24 Jan 2020) |
| EllapsedTime: 165.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: affy.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings affy_1.65.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc-testing/meat/affy.Rcheck’
* using R Under development (unstable) (2019-12-14 r77569)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.65.1’
* 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 ‘affy’ 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘stats:::C_loess_raw’ ‘stats:::C_lowesp’ ‘stats:::C_lowesw’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function calls to a base package:
.C(stats:::C_loess_raw, ...)
.Fortran(stats:::C_lowesp, ...)
.Fortran(stats:::C_lowesw, ...)
Packages should not make .C/.Call/.External/.Fortran calls to a base
package. They are not part of the API, for use only by R itself and
subject to change without notice.
* checking R code for possible problems ... OK
* 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 shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
mas5 36.158 0.068 36.249
MAplot 16.632 0.176 16.813
expresso 15.055 0.032 15.102
ProgressBarText-class 0.935 0.020 16.494
* 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 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.11-bioc-testing/meat/affy.Rcheck/00check.log’
for details.
affy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL affy ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.11-bioc-testing/Rlibs’ * installing *source* package ‘affy’ ... ** using staged installation creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/bbs-3.11-bioc-testing/Rlibs/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c chipbackground.c -o chipbackground.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/bbs-3.11-bioc-testing/Rlibs/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c getall_locations.c -o getall_locations.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/bbs-3.11-bioc-testing/Rlibs/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c mas5calls.c -o mas5calls.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/bbs-3.11-bioc-testing/Rlibs/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rma2.c -o rma2.o gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/home/biocbuild/bbs-3.11-bioc-testing/Rlibs/preprocessCore/include' -I/usr/local/include -fpic -g -O2 -Wall -c rma_common.c -o rma_common.o gcc -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.11-bioc-testing/Rlibs/00LOCK-affy/00new/affy/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (affy)
affy.Rcheck/affy-Ex.timings
| name | user | system | elapsed | |
| AffyBatch-class | 4.716 | 0.135 | 4.886 | |
| AffyRNAdeg | 2.599 | 0.056 | 2.654 | |
| MAplot | 16.632 | 0.176 | 16.813 | |
| ProbeSet-class | 0.57 | 0.00 | 0.57 | |
| ProgressBarText-class | 0.935 | 0.020 | 16.494 | |
| affy-options | 0.000 | 0.000 | 0.001 | |
| barplot.ProbeSet | 0.580 | 0.006 | 0.587 | |
| bgc | 2.679 | 0.096 | 2.779 | |
| cleancdfname | 0.005 | 0.000 | 0.005 | |
| expresso | 15.055 | 0.032 | 15.102 | |
| expressoWidget | 0 | 0 | 0 | |
| fit.li.wong | 0.292 | 0.008 | 0.300 | |
| generateExprSet-methods | 0.643 | 0.000 | 0.643 | |
| generateExprVal-methods | 0.526 | 0.004 | 0.530 | |
| generateExprVal.method.avgdiff | 0.31 | 0.00 | 0.31 | |
| list.celfiles | 0 | 0 | 0 | |
| maffy.subset | 0.018 | 0.000 | 0.019 | |
| mas5 | 36.158 | 0.068 | 36.249 | |
| mas5calls | 1.731 | 0.000 | 1.732 | |
| mva.pairs | 0.080 | 0.000 | 0.081 | |
| normalize-methods | 0.232 | 0.004 | 0.235 | |
| normalize.loess | 0.013 | 0.000 | 0.012 | |
| plot.ProbeSet | 0.013 | 0.000 | 0.013 | |
| plot.density | 0.670 | 0.000 | 0.669 | |
| plotLocation | 2.486 | 0.040 | 2.527 | |
| pmcorrect | 0.492 | 0.000 | 0.492 | |
| ppsetApply | 0.001 | 0.000 | 0.001 | |
| read.affybatch | 2.679 | 0.020 | 2.699 | |
| rma | 2.544 | 0.008 | 2.553 | |
| setAffyOptions | 0.000 | 0.000 | 0.001 | |
| xy2indices | 2.424 | 0.048 | 2.476 | |