Back to Mac ARM64 build report for BioC 3.18 |
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This page was generated on 2024-04-18 11:32:06 -0400 (Thu, 18 Apr 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
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 23/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
affy 1.80.0 (landing page) Robert D. Shear
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | |||||||
To the developers/maintainers of the affy package: - 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. |
Package: affy |
Version: 1.80.0 |
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_1.80.0.tar.gz |
StartedAt: 2024-04-17 05:08:39 -0400 (Wed, 17 Apr 2024) |
EndedAt: 2024-04-17 05:10:59 -0400 (Wed, 17 Apr 2024) |
EllapsedTime: 139.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: affy.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_1.80.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/affy.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: aarch64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘affy/DESCRIPTION’ ... OK * this is package ‘affy’ version ‘1.80.0’ * 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 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 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 16.798 0.193 17.260 MAplot 14.980 0.519 15.558 expresso 6.399 0.120 6.526 fit.li.wong 6.069 0.046 6.142 AffyBatch-class 5.004 0.214 5.241 ProgressBarText-class 1.055 0.027 20.704 * 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, 4 NOTEs See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/affy.Rcheck/00check.log’ for details.
affy.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL affy ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘affy’ ... ** using staged installation creating cache ./config.cache checking how to run the C preprocessor... clang -arch arm64 -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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.3-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 clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.3-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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.3-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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.3-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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DHAVE_ZLIB=1 -I'/Library/Frameworks/R.framework/Versions/4.3-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 -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 -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-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)
affy.Rcheck/affy-Ex.timings
name | user | system | elapsed | |
AffyBatch-class | 5.004 | 0.214 | 5.241 | |
AffyRNAdeg | 1.822 | 0.077 | 1.901 | |
MAplot | 14.980 | 0.519 | 15.558 | |
ProbeSet-class | 0.419 | 0.013 | 0.432 | |
ProgressBarText-class | 1.055 | 0.027 | 20.704 | |
affy-options | 0.000 | 0.000 | 0.001 | |
barplot.ProbeSet | 0.907 | 0.028 | 0.936 | |
bgc | 2.951 | 0.182 | 3.146 | |
cleancdfname | 0.003 | 0.001 | 0.004 | |
expresso | 6.399 | 0.120 | 6.526 | |
expressoWidget | 0 | 0 | 0 | |
fit.li.wong | 6.069 | 0.046 | 6.142 | |
generateExprSet-methods | 0.437 | 0.010 | 0.456 | |
generateExprVal-methods | 0.416 | 0.017 | 0.438 | |
generateExprVal.method.avgdiff | 0.169 | 0.019 | 0.189 | |
list.celfiles | 0 | 0 | 0 | |
maffy.subset | 0.013 | 0.001 | 0.014 | |
mas5 | 16.798 | 0.193 | 17.260 | |
mas5calls | 1.274 | 0.049 | 1.322 | |
mva.pairs | 0.120 | 0.003 | 0.123 | |
normalize-methods | 0.309 | 0.013 | 0.334 | |
normalize.loess | 0.015 | 0.001 | 0.017 | |
plot.ProbeSet | 0.018 | 0.003 | 0.020 | |
plot.density | 1.039 | 0.052 | 1.096 | |
plotLocation | 1.390 | 0.114 | 1.515 | |
pmcorrect | 0.409 | 0.014 | 0.424 | |
ppsetApply | 0.000 | 0.000 | 0.001 | |
read.affybatch | 1.420 | 0.046 | 1.481 | |
rma | 1.701 | 0.052 | 1.756 | |
setAffyOptions | 0 | 0 | 0 | |
xy2indices | 2.020 | 0.163 | 2.246 | |