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This page was generated on 2021-10-26 14:06:15 -0400 (Tue, 26 Oct 2021).

CHECK results for affy on nebbiolo2

To the developers/maintainers of the affy package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/affy.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 23/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.71.0  (landing page)
Rafael A. Irizarry
Snapshot Date: 2021-10-25 14:50:11 -0400 (Mon, 25 Oct 2021)
git_url: https://git.bioconductor.org/packages/affy
git_branch: master
git_last_commit: 0e374ba
git_last_commit_date: 2021-05-19 11:32:58 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  

Summary

Package: affy
Version: 1.71.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings affy_1.71.0.tar.gz
StartedAt: 2021-10-25 19:04:53 -0400 (Mon, 25 Oct 2021)
EndedAt: 2021-10-25 19:06:49 -0400 (Mon, 25 Oct 2021)
EllapsedTime: 115.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: affy.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings affy_1.71.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/affy.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.71.0’
* 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 ‘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                  17.423  0.168  17.591
MAplot                13.097  0.307  13.406
expresso               7.829  0.060   7.890
ProgressBarText-class  0.964  0.012  16.469
* 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-3.14-bioc/meat/affy.Rcheck/00check.log’
for details.



Installation output

affy.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL affy
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* 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-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c getall_locations.c -o getall_locations.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/home/biocbuild/bbs-3.14-bioc/R/library/preprocessCore/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c rma_common.c -o rma_common.o
gcc -shared -L/home/biocbuild/bbs-3.14-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-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/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)

Tests output


Example timings

affy.Rcheck/affy-Ex.timings

nameusersystemelapsed
AffyBatch-class4.1080.1444.252
AffyRNAdeg1.8940.0791.975
MAplot13.097 0.30713.406
ProbeSet-class0.2710.0070.279
ProgressBarText-class 0.964 0.01216.469
affy-options0.0000.0010.000
barplot.ProbeSet0.5480.0110.560
bgc3.7770.0683.844
cleancdfname0.0050.0000.005
expresso7.8290.0607.890
expressoWidget0.0000.0000.001
fit.li.wong3.2600.0723.332
generateExprSet-methods0.3160.0040.320
generateExprVal-methods0.2790.0040.284
generateExprVal.method.avgdiff0.1320.0000.132
list.celfiles0.0010.0000.000
maffy.subset0.0120.0000.012
mas517.423 0.16817.591
mas5calls1.5060.0241.530
mva.pairs0.0790.0040.084
normalize-methods0.2140.0000.215
normalize.loess0.0110.0000.010
plot.ProbeSet0.0110.0000.012
plot.density0.4130.0000.413
plotLocation1.2990.0241.322
pmcorrect0.2410.0000.241
ppsetApply000
read.affybatch1.2660.0081.274
rma1.5780.0081.586
setAffyOptions000
xy2indices1.7610.0361.798