David Mosen-Ansorena
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/seqCNA |
| Branch: RELEASE_3_7 |
| Last Commit: 6aaa1e7 |
| Last Changed Date: 2018-04-30 10:35:30 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:37:26 -0400 (Wed, 17 Oct 2018).
| Package 1346/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| seqCNA 1.26.0 David Mosen-Ansorena
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: seqCNA |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqCNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings seqCNA_1.26.0.tar.gz |
| StartedAt: 2018-10-17 04:45:57 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 04:47:49 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 111.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: seqCNA.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:seqCNA.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings seqCNA_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/seqCNA.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'seqCNA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'seqCNA' version '1.26.0'
* 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 'seqCNA' 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
* 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 ... NOTE
Packages in Depends field not imported from:
'GLAD' 'adehabitatLT' 'doSNOW' 'methods' 'seqCNA.annot'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.autoTrim: no visible global function definition for 'makeCluster'
.autoTrim: no visible global function definition for 'registerDoSNOW'
.autoTrim: no visible global function definition for '%dopar%'
.autoTrim: no visible global function definition for 'foreach'
.autoTrim: no visible global function definition for 'wawotest'
.autoTrim: no visible global function definition for 'quantile'
.autoTrim: no visible global function definition for 'stopCluster'
.autoTrim: no visible global function definition for 'loess'
.autoTrim: no visible global function definition for 'tail'
.buildGenomeInfo: no visible global function definition for
'makeCluster'
.buildGenomeInfo: no visible global function definition for
'registerDoSNOW'
.buildGenomeInfo: no visible global function definition for '%dopar%'
.buildGenomeInfo: no visible global function definition for 'foreach'
.buildGenomeInfo: no visible global function definition for
'stopCluster'
.makeFormula: no visible global function definition for 'as.formula'
.olBarplot: no visible global function definition for 'par'
.olBarplot: no visible global function definition for 'barplot'
.overLapper : <anonymous>: no visible global function definition for
'combn'
.resample: no visible global function definition for 'makeCluster'
.resample: no visible global function definition for 'registerDoSNOW'
.resample: no visible global function definition for '%dopar%'
.resample: no visible global function definition for 'foreach'
.resample: no visible global function definition for 'stopCluster'
.seqnorm: no visible binding for global variable 'head'
.seqnorm: no visible global function definition for 'tail'
.seqnorm: no visible global function definition for 'flush.console'
.seqnorm: no visible binding for global variable 'tail'
.seqnorm: no visible global function definition for 'makeCluster'
.seqnorm: no visible global function definition for 'registerDoSNOW'
.seqnorm: no visible global function definition for '%dopar%'
.seqnorm: no visible global function definition for 'foreach'
.seqnorm: no visible global function definition for 'as.profileCGH'
.seqnorm: no visible global function definition for 'glad'
.seqnorm : <anonymous>: no visible global function definition for
'quantile'
.seqnorm : .getSegmLm: no visible global function definition for
'quantile'
.seqnorm: no visible global function definition for 'predict'
.seqnorm: no visible global function definition for 'median'
.seqnorm : <anonymous>: no visible global function definition for
'median'
.seqnorm: no visible global function definition for 'stopCluster'
.seqnorm: no visible global function definition for 'jpeg'
.seqnorm: no visible global function definition for 'quantile'
.seqnorm: no visible global function definition for 'layout'
.seqnorm: no visible global function definition for 'par'
.seqnorm: no visible global function definition for 'density'
.seqnorm: no visible global function definition for 'plot'
.seqnorm: no visible global function definition for 'points'
.seqnorm: no visible global function definition for 'plot.new'
.seqnorm: no visible global function definition for 'legend'
.seqnorm: no visible global function definition for 'abline'
.seqnorm: no visible global function definition for 'dev.off'
.seqnorm: no visible global function definition for 'lines'
.seqnorm: no visible global function definition for 'smoothScatter'
.seqnorm: no visible global function definition for 'colorRampPalette'
.summary.SeqCNAInfo: no visible global function definition for 'head'
.summary.SeqCNAInfo: no visible global function definition for 'tail'
.vennPlot: no visible global function definition for 'symbols'
.vennPlot: no visible global function definition for 'text'
.vennPlot : plotellipse: no visible global function definition for
'par'
.vennPlot : plotellipse: no visible global function definition for
'plot'
.vennPlot : ellipseVenn: no visible global function definition for
'plot.new'
.vennPlot : ellipseVenn: no visible global function definition for
'text'
applyFilters: no visible global function definition for
'supported.builds'
applyFilters: no visible global function definition for 'data'
applyFilters: no visible global function definition for 'quantile'
applyFilters: no visible global function definition for 'flush.console'
applyFilters: no visible global function definition for 'jpeg'
applyFilters: no visible global function definition for 'layout'
applyFilters: no visible global function definition for 'par'
applyFilters: no visible global function definition for 'smoothScatter'
applyFilters: no visible global function definition for
'colorRampPalette'
applyFilters: no visible global function definition for 'points'
applyFilters: no visible global function definition for 'dev.off'
applyFilters: no visible global function definition for 'density'
applyFilters: no visible global function definition for 'plot'
applyFilters: no visible global function definition for 'rect'
applyFilters: no visible global function definition for 'abline'
applyFilters: no visible global function definition for 'lines'
applyFilters: no visible global function definition for 'text'
plotCNProfile: no visible global function definition for 'jpeg'
plotCNProfile: no visible global function definition for 'par'
plotCNProfile: no visible global function definition for 'quantile'
plotCNProfile: no visible global function definition for
'smoothScatter'
plotCNProfile: no visible global function definition for
'colorRampPalette'
plotCNProfile: no visible global function definition for 'abline'
plotCNProfile: no visible global function definition for 'tail'
plotCNProfile : <anonymous>: no visible global function definition for
'lines'
plotCNProfile: no visible global function definition for 'median'
plotCNProfile: no visible global function definition for 'text'
plotCNProfile: no visible global function definition for 'dev.off'
readSeqsumm: no visible global function definition for
'supported.builds'
readSeqsumm: no visible global function definition for 'flush.console'
readSeqsumm: no visible global function definition for 'read.table'
readSeqsumm: no visible global function definition for 'data'
readSeqsumm: no visible global function definition for 'new'
runGLAD: no visible global function definition for 'flush.console'
runGLAD: no visible global function definition for 'makeCluster'
runGLAD: no visible global function definition for 'registerDoSNOW'
runGLAD: no visible global function definition for '%dopar%'
runGLAD: no visible global function definition for 'foreach'
runGLAD: no visible global function definition for 'as.profileCGH'
runGLAD: no visible global function definition for 'glad'
runGLAD: no visible global function definition for 'stopCluster'
writeCNProfile: no visible global function definition for 'write.table'
summary,SeqCNAInfo: no visible global function definition for 'head'
summary,SeqCNAInfo: no visible global function definition for 'tail'
Undefined global functions or variables:
%dopar% abline as.formula as.profileCGH barplot colorRampPalette
combn data density dev.off flush.console foreach glad head jpeg
layout legend lines loess makeCluster median new par plot plot.new
points predict quantile read.table rect registerDoSNOW smoothScatter
stopCluster supported.builds symbols tail text wawotest write.table
Consider adding
importFrom("grDevices", "colorRampPalette", "dev.off", "jpeg")
importFrom("graphics", "abline", "barplot", "layout", "legend",
"lines", "par", "plot", "plot.new", "points", "rect",
"smoothScatter", "symbols", "text")
importFrom("methods", "new")
importFrom("stats", "as.formula", "density", "loess", "median",
"predict", "quantile")
importFrom("utils", "combn", "data", "flush.console", "head",
"read.table", "tail", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/seqCNA/libs/i386/seqCNA.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 or elapsed time > 5s
user system elapsed
plotCNProfile 0.89 0.10 6.67
writeCNProfile 0.35 0.03 5.59
runGLAD 0.32 0.03 6.00
applyThresholds 0.33 0.01 5.79
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotCNProfile 0.78 0.13 6.16
writeCNProfile 0.41 0.08 5.91
runGLAD 0.37 0.05 5.81
applyThresholds 0.41 0.00 5.75
* 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: 4 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/seqCNA.Rcheck/00check.log'
for details.
seqCNA.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/seqCNA_1.26.0.tar.gz && rm -rf seqCNA.buildbin-libdir && mkdir seqCNA.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=seqCNA.buildbin-libdir seqCNA_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL seqCNA_1.26.0.zip && rm seqCNA_1.26.0.tar.gz seqCNA_1.26.0.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 86548 100 86548 0 0 1286k 0 --:--:-- --:--:-- --:--:-- 1457k
install for i386
* installing *source* package 'seqCNA' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c seqCNA.cpp -o seqCNA.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o seqCNA.dll tmp.def seqCNA.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/seqCNA.buildbin-libdir/seqCNA/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'seqCNA'
finding HTML links ... done
SeqCNAInfo-class html
applyFilters html
applyThresholds html
plotCNProfile html
readSeqsumm html
runGLAD html
runSeqnorm html
runSeqsumm html
seqCNA-package html
seqsumm_HCC1143 html
writeCNProfile html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'seqCNA' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c seqCNA.cpp -o seqCNA.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o seqCNA.dll tmp.def seqCNA.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/seqCNA.buildbin-libdir/seqCNA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'seqCNA' as seqCNA_1.26.0.zip
* DONE (seqCNA)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'seqCNA' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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seqCNA.Rcheck/examples_i386/seqCNA-Ex.timings
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seqCNA.Rcheck/examples_x64/seqCNA-Ex.timings
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