Kieran O'Neill
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/contiBAIT |
| Branch: RELEASE_3_11 |
| Last Commit: 43200c3 |
| Last Changed Date: 2020-05-15 13:49:58 -0400 (Fri, 15 May 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:56:22 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE contiBAIT PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 366/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| contiBAIT 1.16.0 Kieran O'Neill
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |
| Package: contiBAIT |
| Version: 1.16.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:contiBAIT.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings contiBAIT_1.16.0.tar.gz |
| StartedAt: 2020-10-17 02:55:35 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 03:05:48 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 613.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: contiBAIT.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:contiBAIT.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings contiBAIT_1.16.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/contiBAIT.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'contiBAIT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'contiBAIT' version '1.16.0'
* 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 whether package 'contiBAIT' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
See 'C:/Users/biocbuild/bbs-3.11-bioc/meat/contiBAIT.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 6.7Mb
sub-directories of 1Mb or more:
extdata 3.4Mb
libs 2.0Mb
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
Documented arguments not in \usage in documentation object 'plotLGDistances,LinkageGroupList,StrandStateMatrix-method':
'...'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/contiBAIT/libs/i386/contiBAIT.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/contiBAIT/libs/x64/contiBAIT.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
contiBAIT 6.91 0.66 7.56
strandSeqFreqTable 5.49 0.05 5.53
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
contiBAIT 4.83 0.24 5.07
* 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 WARNINGs, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/contiBAIT.Rcheck/00check.log'
for details.
contiBAIT.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/contiBAIT_1.16.0.tar.gz && rm -rf contiBAIT.buildbin-libdir && mkdir contiBAIT.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=contiBAIT.buildbin-libdir contiBAIT_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL contiBAIT_1.16.0.zip && rm contiBAIT_1.16.0.tar.gz contiBAIT_1.16.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 3612k 100 3612k 0 0 33.2M 0 --:--:-- --:--:-- --:--:-- 35.2M
install for i386
* installing *source* package 'contiBAIT' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c buildLinkageGroups.cpp -o buildLinkageGroups.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c computeSim.cpp -o computeSim.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c orderContigsGreedy.cpp -o orderContigsGreedy.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o contiBAIT.dll tmp.def buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/contiBAIT.buildbin-libdir/00LOCK-contiBAIT/00new/contiBAIT/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** help
*** installing help indices
converting help for package 'contiBAIT'
finding HTML links ... done
BAIT html
ChrTable html
ContigOrdering html
LibraryGroupList html
LinkageGroupList html
StrandFreqMatrix html
StrandReadMatrix html
StrandStateList html
StrandStateMatrix html
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method
html
clusterContigs-StrandStateMatrix-method
html
contiBAIT html
exampleChrTable html
exampleContigOrder html
exampleCrickFreq html
exampleDividedChr html
exampleLGList html
exampleLibList html
exampleReadCounts html
exampleStrandFreq html
exampleWCMatrix html
exampleWatsonFreq html
findSexGroups-LinkageGroupList-StrandStateMatrix-method
html
findSimilarLibraries html
fixLinkageGroups html
flipOrderedLinkageGroups html
highlightAssemblyErrors html
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method
html
locateMisorients html
makeBoxPlot html
makeChrTable html
mapGapFromOverlap html
mergeFlankedLGs html
orderAllLinkageGroups html
orderContigsGreedy html
orderContigsTSP html
plotContigOrder html
plotLGDistances-LinkageGroupList-StrandStateMatrix-method
html
plotWCdistribution-StrandFreqMatrix-method
html
preprocessStrandTable-StrandFreqMatrix-method
html
reorientAndMergeLGs html
show-ContigOrdering-method html
show-LibraryGroupList-method html
show-LinkageGroupList-method html
show-OrientationFrame-method html
show-StrandFreqMatrix-method html
show-StrandReadMatrix-method html
show-StrandStateList-method html
show-StrandStateMatrix-method html
strandSeqFreqTable html
thoroughBed html
writeBed html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'contiBAIT' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c buildLinkageGroups.cpp -o buildLinkageGroups.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c computeSim.cpp -o computeSim.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c orderContigsGreedy.cpp -o orderContigsGreedy.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o contiBAIT.dll tmp.def buildLinkageGroups.o computeSim.o orderContigsGreedy.o -lm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/contiBAIT.buildbin-libdir/contiBAIT/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'IRanges::windows' by 'grDevices::windows' when loading 'contiBAIT'
* MD5 sums
packaged installation of 'contiBAIT' as contiBAIT_1.16.0.zip
* DONE (contiBAIT)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'contiBAIT' successfully unpacked and MD5 sums checked
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contiBAIT.Rcheck/examples_i386/contiBAIT-Ex.timings
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contiBAIT.Rcheck/examples_x64/contiBAIT-Ex.timings
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