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CHECK report for affy on malbec2

This page was generated on 2018-10-17 08:20:58 -0400 (Wed, 17 Oct 2018).

Package 17/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.58.0
Rafael A. Irizarry
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/affy
Branch: RELEASE_3_7
Last Commit: 4698231
Last Changed Date: 2018-04-30 10:34:55 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: affy
Version: 1.58.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings affy_1.58.0.tar.gz
StartedAt: 2018-10-15 22:19:22 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 22:21:42 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 139.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: affy.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:affy.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings affy_1.58.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/affy.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.58.0’
* 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
'library' or 'require' call to ‘tkWidgets’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘bg.correct’
* 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 ... NOTE
AllButCelsForReadAffy: no visible global function definition for
  ‘fileBrowser’
AllButCelsForReadAffy: no visible global function definition for
  ‘hasSuffix’
expressoWidget: no visible global function definition for ‘tclVar’
expressoWidget : quit: no visible global function definition for
  ‘tkdestroy’
expressoWidget : end: no visible global function definition for
  ‘tclvalue’
expressoWidget: no visible global function definition for ‘tktoplevel’
expressoWidget: no visible global function definition for ‘tkdestroy’
expressoWidget: no visible global function definition for ‘tktitle<-’
expressoWidget: no visible global function definition for ‘tkpack’
expressoWidget: no visible global function definition for ‘tklabel’
expressoWidget: no visible global function definition for ‘tkframe’
expressoWidget: no visible global function definition for
  ‘dropdownList’
expressoWidget: no visible global function definition for ‘tclvalue’
expressoWidget: no visible global function definition for ‘tkgrid’
expressoWidget: no visible global function definition for
  ‘tkgrid.configure’
expressoWidget: no visible global function definition for ‘tkbutton’
expressoWidget: no visible global function definition for
  ‘tkwait.window’
Undefined global functions or variables:
  dropdownList fileBrowser hasSuffix tclVar tclvalue tkbutton tkdestroy
  tkframe tkgrid tkgrid.configure tklabel tkpack tktitle<- tktoplevel
  tkwait.window
* 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
mas5                  24.876  0.048  25.451
MAplot                11.876  0.152  12.040
expresso              10.784  0.008  10.816
ProgressBarText-class  0.636  0.012  16.143
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/affy.Rcheck/00check.log’
for details.



Installation output

affy.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL affy
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘affy’ ...
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-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c chipbackground.c -o chipbackground.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c mas5calls.c -o mas5calls.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.7-bioc/R/library/preprocessCore/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c rma2.c -o rma2.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -DHAVE_ZLIB=1  -I"/home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/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
* DONE (affy)

Tests output


Example timings

affy.Rcheck/affy-Ex.timings

nameusersystemelapsed
AffyBatch-class2.5520.0602.617
AffyRNAdeg1.4200.0441.470
MAplot11.876 0.15212.040
ProbeSet-class0.2640.0040.270
ProgressBarText-class 0.636 0.01216.143
affy-options0.0000.0000.001
barplot.ProbeSet0.3200.0040.324
bgc2.0400.0362.084
cleancdfname0.0040.0000.004
expresso10.784 0.00810.816
expressoWidget0.0000.0000.001
fit.li.wong0.2000.0080.207
generateExprSet-methods0.3280.0040.332
generateExprVal-methods0.2840.0040.287
generateExprVal.method.avgdiff0.1520.0000.152
list.celfiles0.0040.0000.000
maffy.subset0.0080.0000.010
mas524.876 0.04825.451
mas5calls1.0560.0001.058
mva.pairs0.0800.0040.085
normalize-methods0.2600.0040.266
normalize.loess0.0080.0000.011
plot.ProbeSet0.0120.0000.015
plot.density0.8480.0160.866
plotLocation1.7360.0241.764
pmcorrect0.4360.0040.438
ppsetApply0.0000.0000.001
read.affybatch2.2320.0362.337
rma2.1440.0082.169
setAffyOptions000
xy2indices1.7600.0361.796