Alvaro Cuadros-Inostroza
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/TargetSearch |
| Branch: RELEASE_3_6 |
| Last Commit: 94fa3c1 |
| Last Changed Date: 2017-10-30 12:39:26 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:19:41 -0400 (Thu, 12 Apr 2018).
| Package 1384/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TargetSearch 1.34.0 Alvaro Cuadros-Inostroza
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: TargetSearch |
| Version: 1.34.0 |
| Command: rm -rf TargetSearch.buildbin-libdir TargetSearch.Rcheck && mkdir TargetSearch.buildbin-libdir TargetSearch.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TargetSearch.buildbin-libdir TargetSearch_1.34.0.tar.gz >TargetSearch.Rcheck\00install.out 2>&1 && cp TargetSearch.Rcheck\00install.out TargetSearch-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TargetSearch.buildbin-libdir --install="check:TargetSearch-install.out" --force-multiarch --no-vignettes --timings TargetSearch_1.34.0.tar.gz |
| StartedAt: 2018-04-12 03:32:30 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 03:34:31 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 120.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: TargetSearch.Rcheck |
| Warnings: 1 |
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### Running command:
###
### rm -rf TargetSearch.buildbin-libdir TargetSearch.Rcheck && mkdir TargetSearch.buildbin-libdir TargetSearch.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=TargetSearch.buildbin-libdir TargetSearch_1.34.0.tar.gz >TargetSearch.Rcheck\00install.out 2>&1 && cp TargetSearch.Rcheck\00install.out TargetSearch-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=TargetSearch.buildbin-libdir --install="check:TargetSearch-install.out" --force-multiarch --no-vignettes --timings TargetSearch_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TargetSearch.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TargetSearch/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TargetSearch' version '1.34.0'
* 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
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'TargetSearch' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpemZM7t/R.INSTALL3b181f5c186a/TargetSearch/man/ImportFameSettings.Rd:13: missing file link 'read.delim'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpemZM7t/R.INSTALL3b181f5c186a/TargetSearch/man/ImportSamples.Rd:26: missing file link 'read.delim'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TargetSearch.Rcheck/00install.out' for details.
* 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
* 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
ProfileCleanUp: no visible global function definition for 'as.dist'
plotPeak: no visible global function definition for 'mtext'
plotPeak: no visible global function definition for 'rect'
plotPeak: no visible global function definition for 'gray'
plotPeak: no visible global function definition for 'matlines'
Undefined global functions or variables:
as.dist gray matlines mtext rect
Consider adding
importFrom("grDevices", "gray")
importFrom("graphics", "matlines", "mtext", "rect")
importFrom("stats", "as.dist")
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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.6-bioc/meat/TargetSearch.buildbin-libdir/TargetSearch/libs/i386/TargetSearch.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RIcorrect 10.63 1.11 23.45
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
RIcorrect 10.02 1.09 11.12
* 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: 1 WARNING, 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/TargetSearch.Rcheck/00check.log'
for details.
TargetSearch.Rcheck/00install.out
install for i386
* installing *source* package 'TargetSearch' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c Rinit.c -o Rinit.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c file.c -o file.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c find_peaks.c -o find_peaks.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c getLine.c -o getLine.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c hpf.c -o hpf.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c ncdf.c -o ncdf.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c netcdf_peak_finding.c -o netcdf_peak_finding.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c peakExtraction.c -o peakExtraction.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O3 -Wall -std=gnu99 -mtune=generic -c ppc.c -o ppc.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o TargetSearch.dll tmp.def Rinit.o file.o find_peaks.o getLine.o hpf.o ncdf.o netcdf_peak_finding.o peakExtraction.o ppc.o -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/TargetSearch.buildbin-libdir/TargetSearch/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'TargetSearch'
finding HTML links ... done
FAMEoutliers html
FindPeaks html
ImportFameSettings html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpemZM7t/R.INSTALL3b181f5c186a/TargetSearch/man/ImportFameSettings.Rd:13: missing file link 'read.delim'
ImportLibrary html
ImportSamples html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/RtmpemZM7t/R.INSTALL3b181f5c186a/TargetSearch/man/ImportSamples.Rd:26: missing file link 'read.delim'
NetCDFPeakFinding html
Profile html
ProfileCleanUp html
RIcorrect html
TargetSearch-package html
TargetSearchGUI html
Write.Results html
baseline html
defunct html
file html
fixRI html
medianRILib html
peakCDFextraction html
peakFind html
plotFAME html
plotPeak html
plotPeakSimple html
plotRIdev html
plotSpectra html
quantMatrix html
ri2rt html
riMatrix html
rt2ri html
sampleRI html
tsLib-class html
tsMSdata-class html
tsProfile-class html
tsRim-class html
tsSample-class html
writeLibText html
writeMSP html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'TargetSearch' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c Rinit.c -o Rinit.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c file.c -o file.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c find_peaks.c -o find_peaks.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c getLine.c -o getLine.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c hpf.c -o hpf.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c ncdf.c -o ncdf.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c netcdf_peak_finding.c -o netcdf_peak_finding.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c peakExtraction.c -o peakExtraction.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -O2 -Wall -std=gnu99 -mtune=generic -c ppc.c -o ppc.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o TargetSearch.dll tmp.def Rinit.o file.o find_peaks.o getLine.o hpf.o ncdf.o netcdf_peak_finding.o peakExtraction.o ppc.o -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/TargetSearch.buildbin-libdir/TargetSearch/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TargetSearch' as TargetSearch_1.34.0.zip
* DONE (TargetSearch)
In R CMD INSTALL
In R CMD INSTALL
|
TargetSearch.Rcheck/examples_i386/TargetSearch-Ex.timings
|
TargetSearch.Rcheck/examples_x64/TargetSearch-Ex.timings
|