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This page was generated on 2025-08-04 11:45 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
palomino7Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4565
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4603
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4544
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
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 24/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.86.0  (landing page)
Robert D. Shear
Snapshot Date: 2025-07-31 13:40 -0400 (Thu, 31 Jul 2025)
git_url: https://git.bioconductor.org/packages/affy
git_branch: RELEASE_3_21
git_last_commit: 263e707
git_last_commit_date: 2025-04-15 09:16:06 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for affy on kjohnson1

To the developers/maintainers of the affy package:
- 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 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.

raw results


Summary

Package: affy
Version: 1.86.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:affy.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings affy_1.86.0.tar.gz
StartedAt: 2025-08-01 11:26:41 -0400 (Fri, 01 Aug 2025)
EndedAt: 2025-08-01 11:28:59 -0400 (Fri, 01 Aug 2025)
EllapsedTime: 138.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: affy.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:affy.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings affy_1.86.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/affy.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.86.0’
* 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
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Things done:
      0 (wh:) moved everything related to Cdf-class from 'affy' to 'makecdfenv':
        R/Cdf.R, R/getLocationsData.Cdf.R, locate.name.R, pmormm.R
        R/read.cdffile.R, data/cdf.example.rda, man/Cdf-class.Rd
        man/getLocationsData.Cdf.Rd, man/locate.name.Rd, man/pmormm.Rd
        man/read.cdffile.Rd, src/read_cdffile.c
      o read.affybatch2 reads all cel files together in one big hit
        into an affybatch
      o the baseline in normalize.AffyBatch,invariant can be selected
        using a baseline.type parameter. Also changed "progress" to the 
        more standard "verbose". Seemed to be an error since both PM and
        MM probes were normalized by only PM's where used to establish the 
        normalization, now follows same standard as been introduced for
        normalize.AffyBatch.quantiles.
      o Most normalization routines can now be called with the parameter 
        type which specifies whether to be pmonly, mmonly, both together 
        or both separately. This introduces more consistency to the how
        the normalization routines are actually applied to affybatchs.
      o express() has been completely removed.
* 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) xy2indices.Rd:51: Escaped LaTeX specials: \_ \_
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'AffyBatch-class.Rd':
  ‘[Biobase:class.eSet]{eSet}’

Non-topic package-anchored link(s) in Rd file 'affy.scalevalue.exprSet.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'expresso.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'generateExprSet-methods.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'justrma.Rd':
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
  ‘[Biobase:class.MIAME]{MIAME}’
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'mas5.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

Non-topic package-anchored link(s) in Rd file 'read.affybatch.Rd':
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
  ‘[Biobase:class.MIAME]{MIAME}’

Non-topic package-anchored link(s) in Rd file 'read.probematrix.Rd':
  ‘[Biobase:class.AnnotatedDataFrame]{AnnotatedDataFrame}’
  ‘[Biobase:class.MIAME]{MIAME}’

Non-topic package-anchored link(s) in Rd file 'rma.Rd':
  ‘[Biobase:class.ExpressionSet]{ExpressionSet}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  AffyBatch-class.Rd: normalize
  normalize-methods.Rd: normalize
  normalize.invariantset.Rd: normalize
  normalize.loess.Rd: normalize
  normalize.quantiles.Rd: normalize
  normalize.quantiles.robust.Rd: normalize
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
mas5                  16.181  0.165  16.469
MAplot                15.311  0.500  15.910
expresso               6.790  0.166   7.013
fit.li.wong            4.926  0.064   5.054
ProgressBarText-class  1.168  0.031  20.555
* 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: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/affy.Rcheck/00check.log’
for details.


Installation output

affy.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL affy
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘affy’ ...
** this is package ‘affy’ version ‘1.86.0’
** using staged installation
creating cache ./config.cache
checking how to run the C preprocessor... clang -arch arm64 -std=gnu2x -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
using C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c chipbackground.c -o chipbackground.o
chipbackground.c:119:58: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand]
  if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1==0)){
                                                         ^  ~~~~~~
chipbackground.c:119:58: note: use '&' for a bitwise operation
  if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1==0)){
                                                         ^~
                                                         &
chipbackground.c:119:58: note: remove constant to silence this warning
  if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1==0)){
                                                        ~^~~~~~~~~
chipbackground.c:242:58: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand]
  if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1 ==0)){
                                                         ^  ~~~~~~~
chipbackground.c:242:58: note: use '&' for a bitwise operation
  if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1 ==0)){
                                                         ^~
                                                         &
chipbackground.c:242:58: note: remove constant to silence this warning
  if ((rows == 640) && (cols == 640) && (grid_dim == 16) && (1 ==0)){
                                                        ~^~~~~~~~~~
2 warnings generated.
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c getall_locations.c -o getall_locations.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c mas5calls.c -o mas5calls.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c rma2.c -o rma2.o
clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/preprocessCore/include' -I/opt/R/arm64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c rma_common.c -o rma_common.o
clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/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-class4.3840.2384.663
AffyRNAdeg1.9450.0682.025
MAplot15.311 0.50015.910
ProbeSet-class0.2760.0090.295
ProgressBarText-class 1.168 0.03120.555
affy-options0.0010.0010.000
barplot.ProbeSet0.8700.0240.896
bgc3.1430.2253.405
cleancdfname0.0060.0020.008
expresso6.7900.1667.013
expressoWidget0.0010.0000.001
fit.li.wong4.9260.0645.054
generateExprSet-methods0.4160.0110.429
generateExprVal-methods0.3870.0150.404
generateExprVal.method.avgdiff0.1670.0190.186
list.celfiles000
maffy.subset0.0130.0010.014
mas516.181 0.16516.469
mas5calls1.7420.0731.866
mva.pairs0.1190.0050.127
normalize-methods0.3160.0100.326
normalize.loess0.0130.0020.015
plot.ProbeSet0.0180.0050.022
plot.density0.6130.0760.692
plotLocation1.2990.1221.468
pmcorrect0.3740.0250.403
ppsetApply0.0010.0000.001
read.affybatch1.5340.0581.621
rma1.6980.0561.763
setAffyOptions0.0000.0000.001
xy2indices1.9490.1682.175