Back to Mac ARM64 build report for BioC 3.20 |
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This page was generated on 2024-05-20 11:32:15 -0400 (Mon, 20 May 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4381 |
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 1205/2233 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
methylPipe 1.39.0 (landing page) Mattia Furlan
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | ||||||||
To the developers/maintainers of the methylPipe 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: methylPipe |
Version: 1.39.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylPipe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylPipe_1.39.0.tar.gz |
StartedAt: 2024-05-19 18:46:59 -0400 (Sun, 19 May 2024) |
EndedAt: 2024-05-19 18:55:24 -0400 (Sun, 19 May 2024) |
EllapsedTime: 505.3 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: methylPipe.Rcheck |
Warnings: 2 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:methylPipe.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings methylPipe_1.39.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/methylPipe.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-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 Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘methylPipe/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘methylPipe’ version ‘1.39.0’ * 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 ‘methylPipe’ 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 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE findPMDs,BSdata : PMDchr: no visible global function definition for 'segmentPMDs' show,BSdata: no visible global function definition for 'organism' show,BSdataSet: no visible global function definition for 'organism' Undefined global functions or variables: organism segmentPMDs * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Undocumented S4 methods: generic '[' and siglist 'BSdataSet,ANY,ANY,ANY' generic '[' and siglist 'GElist,ANY,ANY,ANY' generic '[[<-' and siglist 'BSdataSet,ANY,ANY,ANY' generic '[[<-' and siglist 'GElist,ANY,ANY,ANY' All user-level objects in a package (including S4 classes and methods) should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... 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 ... WARNING Found the following significant warnings: Warning: working directory was changed to '/private/tmp/RtmpRZfUvg', resetting Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotMeth 26.123 0.547 33.587 findDMR 1.036 1.205 30.832 methstats 0.891 0.152 21.772 findPMDs 0.180 0.097 23.876 * 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: 2 WARNINGs, 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/methylPipe.Rcheck/00check.log’ for details.
methylPipe.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL methylPipe ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘methylPipe’ ... ** 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 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_methylPipe.c -o R_init_methylPipe.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c binning.c -o binning.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 methylPipe.so R_init_methylPipe.o binning.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/00LOCK-methylPipe/00new/methylPipe/libs ** R ** exec ** 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 (methylPipe)
methylPipe.Rcheck/methylPipe-Ex.timings
name | user | system | elapsed | |
BSdata-class | 0.246 | 0.020 | 0.267 | |
BSdataSet-class | 0.149 | 0.007 | 0.157 | |
BSprepare | 0 | 0 | 0 | |
GEcollection-class | 3.091 | 0.069 | 3.165 | |
GElist-class | 0.032 | 0.002 | 0.034 | |
chiCombP | 0 | 0 | 0 | |
consolidateDMRs | 0.189 | 0.002 | 0.192 | |
extractBinGRanges | 0.018 | 0.001 | 0.019 | |
findDMR | 1.036 | 1.205 | 30.832 | |
findPMDs | 0.180 | 0.097 | 23.876 | |
getCpos | 0.105 | 0.006 | 0.111 | |
getCposDensity | 0.094 | 0.006 | 0.099 | |
mCsmoothing | 0.347 | 0.011 | 0.358 | |
mapBSdata2GRanges | 0.860 | 0.014 | 0.896 | |
methstats | 0.891 | 0.152 | 21.772 | |
plotMeth | 26.123 | 0.547 | 33.587 | |
pool.reads | 0 | 0 | 0 | |
process.hmc | 0 | 0 | 0 | |
profileDNAmetBin | 1.427 | 0.090 | 1.516 | |