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This page was generated on 2024-02-28 11:38:32 -0500 (Wed, 28 Feb 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4671
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4411
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4438
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4414
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 23/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affy 1.81.0  (landing page)
Robert D. Shear
Snapshot Date: 2024-02-26 14:39:26 -0500 (Mon, 26 Feb 2024)
git_url: https://git.bioconductor.org/packages/affy
git_branch: devel
git_last_commit: 928e160
git_last_commit_date: 2023-10-24 09:31:51 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for affy on merida1


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: 1.81.0
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_1.81.0.tar.gz
StartedAt: 2024-02-27 01:43:39 -0500 (Tue, 27 Feb 2024)
EndedAt: 2024-02-27 01:47:50 -0500 (Tue, 27 Feb 2024)
EllapsedTime: 250.4 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_1.81.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/affy.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.81.0’
* 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 14.0.0 (clang-1400.0.29.202)’
* 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 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 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 ... 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 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                  50.445  0.475  54.926
expresso              19.571  0.287  22.264
MAplot                16.857  1.107  20.499
AffyBatch-class        8.611  0.410   9.410
fit.li.wong            5.713  0.143   6.375
bgc                    4.087  0.441   5.125
ProgressBarText-class  1.205  0.047  18.536
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/Resources/library’
* installing *source* package ‘affy’ ...
** using staged installation
creating cache ./config.cache
checking how to run the C preprocessor... clang -arch x86_64 -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 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/preprocessCore/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c chipbackground.c -o chipbackground.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/preprocessCore/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c getall_locations.c -o getall_locations.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/preprocessCore/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c mas5calls.c -o mas5calls.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/preprocessCore/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c rma2.c -o rma2.o
clang -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/preprocessCore/include' -I/opt/R/x86_64/include   -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c rma_common.c -o rma_common.o
clang -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/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-class8.6110.4109.410
AffyRNAdeg3.0580.1853.534
MAplot16.857 1.10720.499
ProbeSet-class0.5220.0210.593
ProgressBarText-class 1.205 0.04718.536
affy-options0.0000.0010.002
barplot.ProbeSet0.9930.0351.164
bgc4.0870.4415.125
cleancdfname0.0090.0030.013
expresso19.571 0.28722.264
expressoWidget0.0010.0010.002
fit.li.wong5.7130.1436.375
generateExprSet-methods0.6900.0180.741
generateExprVal-methods0.5710.0240.623
generateExprVal.method.avgdiff0.4300.0490.528
list.celfiles0.0000.0010.001
maffy.subset0.0200.0020.033
mas550.445 0.47554.926
mas5calls1.9200.0842.186
mva.pairs0.1240.0060.138
normalize-methods0.4190.0100.474
normalize.loess0.0190.0020.021
plot.ProbeSet0.0190.0040.026
plot.density0.6930.0400.762
plotLocation2.1170.2352.548
pmcorrect0.4990.0260.561
ppsetApply0.0010.0010.002
read.affybatch2.9470.1373.618
rma2.0870.0392.236
setAffyOptions0.0000.0000.001
xy2indices2.7030.2583.252