Ramon Diaz-Uriarte
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/ADaCGH2 |
| Branch: RELEASE_3_7 |
| Last Commit: 16602d5 |
| Last Changed Date: 2018-04-30 10:35:15 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:35:01 -0400 (Wed, 17 Oct 2018).
| Package 13/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ADaCGH2 2.20.0 Ramon Diaz-Uriarte
| 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 | OK | OK | |
| Package: ADaCGH2 |
| Version: 2.20.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ADaCGH2.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ADaCGH2_2.20.0.tar.gz |
| StartedAt: 2018-10-17 00:25:43 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 00:30:55 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 312.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ADaCGH2.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ADaCGH2.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings ADaCGH2_2.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/ADaCGH2.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 'ADaCGH2/DESCRIPTION' ... OK
* this is package 'ADaCGH2' version '2.20.0'
* 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 ... 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
* 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 ... 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-3.7-bioc/R/library/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 22.52 0.11 23.75
pSegment 14.47 0.00 14.47
outputToCGHregions 10.15 0.05 10.43
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
pChromPlot 25.34 0.03 25.37
pSegment 22.82 0.00 22.81
outputToCGHregions 11.11 0.11 11.22
inputToADaCGH 6.50 0.08 6.85
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/ADaCGH2.Rcheck/00check.log'
for details.
ADaCGH2.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/ADaCGH2_2.20.0.tar.gz && rm -rf ADaCGH2.buildbin-libdir && mkdir ADaCGH2.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ADaCGH2.buildbin-libdir ADaCGH2_2.20.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL ADaCGH2_2.20.0.zip && rm ADaCGH2_2.20.0.tar.gz ADaCGH2_2.20.0.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 720k 100 720k 0 0 13.4M 0 --:--:-- --:--:-- --:--:-- 15.3M
install for i386
* installing *source* package 'ADaCGH2' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/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/gcc -shared -s -static-libgcc -o ADaCGH2.dll tmp.def init.o r_haarseg.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/ADaCGH2.buildbin-libdir/ADaCGH2/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ADaCGH2'
finding HTML links ... done
cutFile html
inputEx html
inputToADaCGH html
finding level-2 HTML links ... done
outputToCGHregions html
pChromPlot html
pSegment html
** building package indices
** installing vignettes
'ADaCGH2.Rnw' using 'latin1'
** 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˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/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˜1.7-B/R/include" -DNDEBUG -I"C:/extsoft/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/gcc -shared -s -static-libgcc -o ADaCGH2.dll tmp.def init.o r_haarseg.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/ADaCGH2.buildbin-libdir/ADaCGH2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ADaCGH2' as ADaCGH2_2.20.0.zip
* DONE (ADaCGH2)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'ADaCGH2' successfully unpacked and MD5 sums checked
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
|