Kieran O'Neill
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/contiBAIT |
| Branch: RELEASE_3_9 |
| Last Commit: 406d05f |
| Last Changed Date: 2019-05-02 11:54:00 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:57:13 -0400 (Wed, 16 Oct 2019).
| Package 339/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| contiBAIT 1.12.0 Kieran O'Neill
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: contiBAIT |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings contiBAIT_1.12.0.tar.gz |
| StartedAt: 2019-10-16 01:45:31 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:53:16 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 465.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: contiBAIT.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:contiBAIT.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings contiBAIT_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/contiBAIT.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘contiBAIT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘contiBAIT’ version ‘1.12.0’
* 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 ‘contiBAIT’ can be installed ... OK
* 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 ... NOTE
ideogramPlot.func: no visible binding for global variable ‘w’
ideogramPlot.func: no visible binding for global variable ‘w2’
makeChrTable: no visible global function definition for ‘queryHits’
makeChrTable: no visible global function definition for ‘subjectHits’
orderContigsGreedy: no visible global function definition for
‘makeCluster’
orderContigsGreedy: no visible global function definition for
‘clusterCall’
orderContigsGreedy: no visible global function definition for
‘stopCluster’
strandSeqFreqTable: no visible global function definition for
‘queryHits’
strandSeqFreqTable: no visible global function definition for
‘subjectHits’
ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible
binding for global variable ‘w’
ideogramPlot,StrandReadMatrix-StrandReadMatrix-ChrTable: no visible
binding for global variable ‘w2’
Undefined global functions or variables:
clusterCall makeCluster queryHits stopCluster subjectHits w w2
* 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 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 or elapsed time > 5s
user system elapsed
contiBAIT 8.102 0.409 8.543
strandSeqFreqTable 5.138 0.073 5.211
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/contiBAIT.Rcheck/00check.log’
for details.
contiBAIT.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL contiBAIT ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘contiBAIT’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c buildLinkageGroups.cpp -o buildLinkageGroups.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c computeSim.cpp -o computeSim.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/BH/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c orderContigsGreedy.cpp -o orderContigsGreedy.o clang++ -std=gnu++11 -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 contiBAIT.so buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-contiBAIT/00new/contiBAIT/libs ** R ** data ** 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 (contiBAIT)
contiBAIT.Rcheck/contiBAIT-Ex.timings
| name | user | system | elapsed | |
| BAIT | 0.001 | 0.000 | 0.001 | |
| ContigOrdering | 0.003 | 0.000 | 0.003 | |
| LibraryGroupList | 0.019 | 0.003 | 0.021 | |
| LinkageGroupList | 0.002 | 0.001 | 0.002 | |
| StrandFreqMatrix | 0.038 | 0.015 | 0.053 | |
| StrandReadMatrix | 0.018 | 0.003 | 0.021 | |
| StrandStateMatrix | 0.005 | 0.000 | 0.005 | |
| barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method | 0.805 | 0.025 | 0.830 | |
| clusterContigs-StrandStateMatrix-method | 0.036 | 0.007 | 0.044 | |
| contiBAIT | 8.102 | 0.409 | 8.543 | |
| findSimilarLibraries | 4.222 | 0.133 | 4.357 | |
| ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method | 3.032 | 0.134 | 3.167 | |
| makeBoxPlot | 0.036 | 0.008 | 0.046 | |
| makeChrTable | 1.240 | 0.006 | 1.246 | |
| orderAllLinkageGroups | 2.106 | 0.132 | 2.238 | |
| plotContigOrder | 0.467 | 0.004 | 0.471 | |
| plotLGDistances-LinkageGroupList-StrandStateMatrix-method | 0.197 | 0.010 | 0.209 | |
| plotWCdistribution-StrandFreqMatrix-method | 0.085 | 0.012 | 0.099 | |
| preprocessStrandTable-StrandFreqMatrix-method | 0.333 | 0.008 | 0.341 | |
| reorientAndMergeLGs | 0.191 | 0.006 | 0.196 | |
| strandSeqFreqTable | 5.138 | 0.073 | 5.211 | |
| thoroughBed | 0.039 | 0.005 | 0.044 | |
| writeBed | 0.001 | 0.000 | 0.000 | |