Ramon Diaz-Uriarte
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/ADaCGH2 |
| Branch: RELEASE_3_6 |
| Last Commit: 813e6ff |
| Last Changed Date: 2017-10-30 12:39:31 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:20:29 -0400 (Thu, 12 Apr 2018).
| Package 13/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ADaCGH2 2.18.0 Ramon Diaz-Uriarte
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ WARNINGS ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: ADaCGH2 |
| Version: 2.18.0 |
| Command: rm -rf ADaCGH2.buildbin-libdir ADaCGH2.Rcheck && mkdir ADaCGH2.buildbin-libdir ADaCGH2.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ADaCGH2.buildbin-libdir ADaCGH2_2.18.0.tar.gz >ADaCGH2.Rcheck\00install.out 2>&1 && cp ADaCGH2.Rcheck\00install.out ADaCGH2-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ADaCGH2.buildbin-libdir --install="check:ADaCGH2-install.out" --force-multiarch --no-vignettes --timings ADaCGH2_2.18.0.tar.gz |
| StartedAt: 2018-04-11 22:04:49 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:11:04 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 375.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: ADaCGH2.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### rm -rf ADaCGH2.buildbin-libdir ADaCGH2.Rcheck && mkdir ADaCGH2.buildbin-libdir ADaCGH2.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=ADaCGH2.buildbin-libdir ADaCGH2_2.18.0.tar.gz >ADaCGH2.Rcheck\00install.out 2>&1 && cp ADaCGH2.Rcheck\00install.out ADaCGH2-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=ADaCGH2.buildbin-libdir --install="check:ADaCGH2-install.out" --force-multiarch --no-vignettes --timings ADaCGH2_2.18.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ADaCGH2.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 'ADaCGH2/DESCRIPTION' ... OK
* this is package 'ADaCGH2' version '2.18.0'
* 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 'ADaCGH2' can be installed ... WARNING
Found the following significant warnings:
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/inputToADaCGH.Rd:45: missing file link 'as.MAList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/inputToADaCGH.Rd:46: missing file link 'dim.SegList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/inputToADaCGH.Rd:154: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/pChromPlot.Rd:126: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/pChromPlot.Rd:142: missing file link 'clusterApplyLB'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/pChromPlot.Rd:144: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/pSegment.Rd:163: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/pSegment.Rd:174: missing file link 'clusterApplyLB'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/pSegment.Rd:177: missing file link 'mclapply'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/ADaCGH2.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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 ... OK
* 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-3.6-bioc/meat/ADaCGH2.buildbin-libdir/ADaCGH2/libs/i386/ADaCGH2.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
pChromPlot 14.19 0.02 15.35
pSegment 10.67 0.00 10.67
outputToCGHregions 6.55 0.11 6.68
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
pChromPlot 20.11 0.11 26.72
pSegment 17.22 0.00 17.22
outputToCGHregions 9.36 0.06 9.42
* 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, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/ADaCGH2.Rcheck/00check.log'
for details.
ADaCGH2.Rcheck/00install.out
install for i386
* installing *source* package 'ADaCGH2' ...
** 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 init.c -o init.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 r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:65:12: warning: unused variable 'totalNorm' [-Wunused-variable]
double totalNorm;
^
r_haarseg.c: In function 'ad_FindLocalPeaks':
r_haarseg.c:152:8: warning: "/*" within comment [-Wcomment]
}/* for j */
^
r_haarseg.c:176:8: warning: "/*" within comment [-Wcomment]
}/* for j */
^
r_haarseg.c:128:9: warning: unused variable 'j' [-Wunused-variable]
int k,j;
^
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:97:27: warning: 'highNonNormed' may be used uninitialized in this function [-Wmaybe-uninitialized]
highNonNormed += signal[highEnd]*weight[highEnd] - signal[k-1]*weight[k-1];
^
r_haarseg.c:96:26: warning: 'lowNonNormed' may be used uninitialized in this function [-Wmaybe-uninitialized]
lowNonNormed += signal[lowEnd]*weight[lowEnd] - signal[k-1]*weight[k-1];
^
r_haarseg.c:99:27: warning: 'highWeightSum' may be used uninitialized in this function [-Wmaybe-uninitialized]
highWeightSum += weight[highEnd] - weight[k-1];
^
r_haarseg.c:98:26: warning: 'lowWeightSum' may be used uninitialized in this function [-Wmaybe-uninitialized]
lowWeightSum += weight[k-1] - weight[lowEnd];
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o ADaCGH2.dll tmp.def init.o r_haarseg.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/ADaCGH2.buildbin-libdir/ADaCGH2/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'ADaCGH2'
finding HTML links ... done
cutFile html
inputEx html
inputToADaCGH html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/inputToADaCGH.Rd:45: missing file link 'as.MAList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/inputToADaCGH.Rd:46: missing file link 'dim.SegList'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/inputToADaCGH.Rd:154: missing file link 'mclapply'
outputToCGHregions html
pChromPlot html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/pChromPlot.Rd:126: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/pChromPlot.Rd:142: missing file link 'clusterApplyLB'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/pChromPlot.Rd:144: missing file link 'mclapply'
pSegment html
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/pSegment.Rd:163: missing file link 'mclapply'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/pSegment.Rd:174: missing file link 'clusterApplyLB'
Rd warning: C:/Users/biocbuild/bbs-3.6-bioc/tmpdir/Rtmpa4ek4f/R.INSTALL2070102a2399/ADaCGH2/man/pSegment.Rd:177: missing file link 'mclapply'
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'ADaCGH2' ...
** 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 init.c -o init.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 r_haarseg.c -o r_haarseg.o
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:65:12: warning: unused variable 'totalNorm' [-Wunused-variable]
double totalNorm;
^
r_haarseg.c: In function 'ad_FindLocalPeaks':
r_haarseg.c:152:8: warning: "/*" within comment [-Wcomment]
}/* for j */
^
r_haarseg.c:176:8: warning: "/*" within comment [-Wcomment]
}/* for j */
^
r_haarseg.c:128:9: warning: unused variable 'j' [-Wunused-variable]
int k,j;
^
r_haarseg.c: In function 'ad_HaarConv':
r_haarseg.c:97:27: warning: 'highNonNormed' may be used uninitialized in this function [-Wmaybe-uninitialized]
highNonNormed += signal[highEnd]*weight[highEnd] - signal[k-1]*weight[k-1];
^
r_haarseg.c:96:26: warning: 'lowNonNormed' may be used uninitialized in this function [-Wmaybe-uninitialized]
lowNonNormed += signal[lowEnd]*weight[lowEnd] - signal[k-1]*weight[k-1];
^
r_haarseg.c:99:27: warning: 'highWeightSum' may be used uninitialized in this function [-Wmaybe-uninitialized]
highWeightSum += weight[highEnd] - weight[k-1];
^
r_haarseg.c:98:26: warning: 'lowWeightSum' may be used uninitialized in this function [-Wmaybe-uninitialized]
lowWeightSum += weight[k-1] - weight[lowEnd];
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o ADaCGH2.dll tmp.def init.o r_haarseg.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/ADaCGH2.buildbin-libdir/ADaCGH2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ADaCGH2' as ADaCGH2_2.18.0.zip
* DONE (ADaCGH2)
In R CMD INSTALL
In R CMD INSTALL
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ADaCGH2.Rcheck/examples_i386/ADaCGH2-Ex.timings
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ADaCGH2.Rcheck/examples_x64/ADaCGH2-Ex.timings
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