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 |
---|---|---|---|---|
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 12/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
aCGH 1.80.0 (landing page) Peter Dimitrov
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK | ||||||||
To the developers/maintainers of the aCGH 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: aCGH |
Version: 1.80.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:aCGH.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings aCGH_1.80.0.tar.gz |
StartedAt: 2024-04-17 05:02:53 -0400 (Wed, 17 Apr 2024) |
EndedAt: 2024-04-17 05:04:20 -0400 (Wed, 17 Apr 2024) |
EllapsedTime: 87.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: aCGH.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:aCGH.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings aCGH_1.80.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/aCGH.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 ‘aCGH/DESCRIPTION’ ... OK * this is package ‘aCGH’ 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 ‘aCGH’ 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 ... 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * 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 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 * 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 NOTE See ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/aCGH.Rcheck/00check.log’ for details.
aCGH.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL aCGH ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’ * installing *source* package ‘aCGH’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSEDOUBLE -g3 -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c hmm.cpp -o hmm.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-aCGH/00new/aCGH/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 (aCGH)
aCGH.Rcheck/aCGH-Ex.timings
name | user | system | elapsed | |
aCGH | 1.482 | 0.134 | 1.646 | |
aCGH.process | 0.050 | 0.002 | 0.053 | |
aCGH.read.Sprocs | 0.240 | 0.009 | 0.255 | |
clusterGenome | 1.162 | 0.103 | 1.296 | |
colorectal | 0.585 | 0.018 | 0.616 | |
fga.func | 0.299 | 0.011 | 0.316 | |
find.hmm.states | 0.603 | 0.014 | 0.621 | |
gainLoss | 1.395 | 0.030 | 1.427 | |
heatmap | 0.587 | 0.019 | 0.608 | |
impute.HMM | 0.302 | 0.015 | 0.317 | |
impute.lowess | 0.052 | 0.009 | 0.062 | |
mergeLevels | 0.088 | 0.013 | 0.100 | |
plotFreqStat | 3.164 | 0.064 | 3.235 | |
plotGenome | 1.726 | 0.089 | 1.843 | |
plotHmmStates | 0.372 | 0.027 | 0.407 | |
plotSummaryProfile | 0.976 | 0.053 | 1.034 | |
summarize.clones | 0.323 | 0.014 | 0.337 | |
threshold.func | 0.283 | 0.020 | 0.303 | |