Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-24 09:07 -0400 (Wed, 24 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4747 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4489 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4518 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4467 |
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 341/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ChIPseqR 1.58.0 (landing page) Peter Humburg
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the ChIPseqR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ChIPseqR.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. |
Package: ChIPseqR |
Version: 1.58.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPseqR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPseqR_1.58.0.tar.gz |
StartedAt: 2024-07-22 15:08:27 -0400 (Mon, 22 Jul 2024) |
EndedAt: 2024-07-22 15:13:44 -0400 (Mon, 22 Jul 2024) |
EllapsedTime: 316.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ChIPseqR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ChIPseqR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ChIPseqR_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/ChIPseqR.Rcheck’ * using R version 4.4.1 (2024-06-14) * 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 ‘ChIPseqR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ChIPseqR’ version ‘1.58.0’ * 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 ‘ChIPseqR’ 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 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 .fixCounts: no visible global function definition for ‘runLength’ .fixCounts: no visible global function definition for ‘runValue’ getBindLen: no visible global function definition for ‘window’ pickPeak: no visible global function definition for ‘start’ pickPeak: no visible global function definition for ‘runLength’ pickPeak : <anonymous>: no visible global function definition for ‘window’ [[,BindScore-ANY-numeric: no visible global function definition for ‘window’ decompress,Rle: no visible global function definition for ‘runValue’ decompress,RleList : <anonymous>: no visible global function definition for ‘runValue’ initialize,RLEBindScore : <anonymous>: no visible global function definition for ‘Rle’ initialize,RLEBindScore : <anonymous>: no visible global function definition for ‘runValue’ initialize,RLEBindScore : <anonymous>: no visible global function definition for ‘runValue<-’ plot,RLEReadCounts-missing : <anonymous>: no visible global function definition for ‘window’ Undefined global functions or variables: Rle runLength runValue runValue<- start window Consider adding importFrom("stats", "start", "window") to your NAMESPACE file. * 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 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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed alignFeature 10.346 2.522 13.229 RLEBindScore-class 7.192 0.211 7.523 BindScore 7.053 0.220 7.410 simpleNucCall 5.877 0.228 6.348 callBindingSites 4.928 0.229 5.374 * 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 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/ChIPseqR.Rcheck/00check.log’ for details.
ChIPseqR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ChIPseqR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘ChIPseqR’ ... ** 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 startScore.c -o startScore.o startScore.c:66:15: warning: unused variable 'tmp_stat' [-Wunused-variable] double stat, tmp_stat; ^ 1 warning generated. 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 ChIPseqR.so startScore.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-ChIPseqR/00new/ChIPseqR/libs ** R ** 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 (ChIPseqR)
ChIPseqR.Rcheck/ChIPseqR-Ex.timings
name | user | system | elapsed | |
BindScore | 7.053 | 0.220 | 7.410 | |
ChIPseqR-package | 0.000 | 0.000 | 0.001 | |
RLEBindScore-class | 7.192 | 0.211 | 7.523 | |
RLEReadCounts-class | 0.027 | 0.001 | 0.028 | |
ReadCounts | 0.029 | 0.001 | 0.031 | |
alignFeature | 10.346 | 2.522 | 13.229 | |
callBindingSites | 4.928 | 0.229 | 5.374 | |
pos2gff | 0.005 | 0.000 | 0.006 | |
simpleNucCall | 5.877 | 0.228 | 6.348 | |
strandPileup | 0.01 | 0.00 | 0.01 | |
windowCounts | 0.170 | 0.002 | 0.173 | |