Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:41 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the maigesPack package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/maigesPack.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1024/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
maigesPack 1.56.0 (landing page) Gustavo H. Esteves
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: maigesPack |
Version: 1.56.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings --no-examples maigesPack_1.56.0.tar.gz |
StartedAt: 2021-10-14 20:37:38 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 20:39:06 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 87.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: maigesPack.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:maigesPack.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings --no-examples maigesPack_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/maigesPack.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using options ‘--no-examples --no-vignettes’ * checking for file ‘maigesPack/DESCRIPTION’ ... OK * this is package ‘maigesPack’ version ‘1.56.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘maigesPack’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Malformed Description field: should contain one or more complete sentences. * 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 ... NOTE 'library' or 'require' calls in package code: ‘OLIN’ ‘annotate’ ‘rgl’ Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE activeMod: no visible global function definition for ‘sessionInfo’ activeModScoreHTML: no visible binding for global variable ‘data’ activeNet: no visible global function definition for ‘sessionInfo’ activeNetScoreHTML: no visible binding for global variable ‘data’ blackBlue: no visible global function definition for ‘col2rgb’ blackBlue: no visible global function definition for ‘rgb’ classifyKNN: no visible global function definition for ‘sessionInfo’ classifyKNNsc: no visible global function definition for ‘sessionInfo’ classifyLDA: no visible global function definition for ‘sessionInfo’ classifyLDAsc: no visible global function definition for ‘sessionInfo’ classifySVM: no visible global function definition for ‘sessionInfo’ classifySVMsc: no visible global function definition for ‘sessionInfo’ createMaigesRaw: no visible global function definition for ‘sessionInfo’ createTDMS: no visible global function definition for ‘write.table’ deGenes2by2BootT: no visible global function definition for ‘sessionInfo’ deGenes2by2Ttest: no visible global function definition for ‘sessionInfo’ deGenes2by2Wilcox: no visible global function definition for ‘sessionInfo’ deGenesANOVA: no visible global function definition for ‘sessionInfo’ designANOVA: no visible global function definition for ‘sessionInfo’ greenRed: no visible global function definition for ‘col2rgb’ greenRed: no visible global function definition for ‘rgb’ loadData: no visible global function definition for ‘read.table’ loadData: no visible global function definition for ‘sessionInfo’ normLoc: no visible global function definition for ‘sessionInfo’ normOLIN: no visible global function definition for ‘sessionInfo’ normRepLoess: no visible global function definition for ‘sessionInfo’ normScaleLimma: no visible global function definition for ‘sessionInfo’ normScaleMarray: no visible global function definition for ‘sessionInfo’ print.maiges: no visible global function definition for ‘str’ print.maigesANOVA: no visible global function definition for ‘str’ print.maigesPreRaw: no visible global function definition for ‘str’ print.maigesRaw: no visible global function definition for ‘str’ relNet2TGF.maigesRelNetB: no visible global function definition for ‘write.table’ relNet2TGF.maigesRelNetM: no visible global function definition for ‘write.table’ relNetworkB: no visible global function definition for ‘sessionInfo’ relNetworkM: no visible global function definition for ‘sessionInfo’ selSpots: no visible global function definition for ‘sessionInfo’ summarizeReplicates: no visible global function definition for ‘sessionInfo’ tableClass: no visible global function definition for ‘write.table’ tablesDE: no visible global function definition for ‘setRepository’ tablesDE: no visible global function definition for ‘write.table’ Undefined global functions or variables: col2rgb data read.table rgb sessionInfo setRepository str write.table Consider adding importFrom("grDevices", "col2rgb", "rgb") importFrom("utils", "data", "read.table", "sessionInfo", "str", "write.table") 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 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 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 ... SKIPPED * 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: 5 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/maigesPack.Rcheck/00check.log’ for details.
maigesPack.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL maigesPack ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘maigesPack’ ... ** using staged installation ** libs clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c Minfo.c -o Minfo.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c bootstrapT.c -o bootstrapT.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c register.c -o register.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c robustCorr.c -o robustCorr.o clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c stats.c -o stats.o clang -mmacosx-version-min=10.13 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o maigesPack.so Minfo.o bootstrapT.o register.o robustCorr.o stats.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/library/00LOCK-maigesPack/00new/maigesPack/libs ** R ** data ** 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 (maigesPack)