Guenter Klambauer
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/cn.mops |
| Branch: RELEASE_3_8 |
| Last Commit: f953d10 |
| Last Changed Date: 2018-10-30 11:41:48 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:21:57 -0400 (Sat, 13 Apr 2019).
| Package 285/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cn.mops 1.28.0 Guenter Klambauer
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: cn.mops |
| Version: 1.28.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cn.mops.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cn.mops_1.28.0.tar.gz |
| StartedAt: 2019-04-13 01:18:49 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 01:25:47 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 417.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cn.mops.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cn.mops.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings cn.mops_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/cn.mops.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cn.mops/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cn.mops' version '1.28.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 'cn.mops' 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-3.8-bioc/R/library/cn.mops/libs/i386/cn.mops.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
referencecn.mops 18.36 0.03 28.48
calcFractionalCopyNumbers-CNVDetectionResult-method 13.18 0.02 13.19
calcFractionalCopyNumbers 11.64 0.03 11.67
cn.mops 9.47 0.18 22.05
haplocn.mops 0.98 0.02 10.70
getReadCountsFromBAM 0.41 0.00 7.90
getSegmentReadCountsFromBAM 0.22 0.02 5.13
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
referencecn.mops 17.82 0.03 30.57
calcFractionalCopyNumbers-CNVDetectionResult-method 9.14 0.04 9.19
calcFractionalCopyNumbers 9.04 0.00 9.04
cn.mops 8.24 0.20 21.18
haplocn.mops 1.36 0.02 10.03
getReadCountsFromBAM 0.48 0.00 6.35
getSegmentReadCountsFromBAM 0.24 0.00 5.40
* 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-3.8-bioc/meat/cn.mops.Rcheck/00check.log'
for details.
cn.mops.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/cn.mops_1.28.0.tar.gz && rm -rf cn.mops.buildbin-libdir && mkdir cn.mops.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cn.mops.buildbin-libdir cn.mops_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL cn.mops_1.28.0.zip && rm cn.mops_1.28.0.tar.gz cn.mops_1.28.0.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
17 634k 17 112k 0 0 407k 0 0:00:01 --:--:-- 0:00:01 411k
100 634k 100 634k 0 0 2271k 0 --:--:-- --:--:-- --:--:-- 2292k
install for i386
* installing *source* package 'cn.mops' ...
** libs
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c R_init_cnmops.c -o R_init_cnmops.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cnmops.cpp -o cnmops.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
double globalMean,globalSd,diff,M2,globalVariance;
^
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
double oldStatistic, meanLeft,meanRight,varLeft,varRight;
^
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
^
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
double newPValue, maxPValue,oldPValue,maxIdx;
^
In file included from segment.cpp:10:0:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rmath.h:212:15: warning: unused variable 'Rf_beta' [-Wunused-variable]
#define beta Rf_beta
^
segment.cpp:64:9: note: in expansion of macro 'beta'
double beta,nn;
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cn.mops'
finding HTML links ... done
CNVDetectionResult html
CNVRanges html
X html
XRanges html
calcFractionalCopyNumbers-CNVDetectionResult-method
html
calcFractionalCopyNumbers html
calcIntegerCopyNumbers-CNVDetectionResult-method
html
calcIntegerCopyNumbers html
cn.mops html
cnvr-CNVDetectionResult-method html
cnvr html
cnvs-CNVDetectionResult-method html
cnvs html
exomeCounts html
exomecn.mops html
getReadCountsFromBAM html
getSegmentReadCountsFromBAM html
gr-CNVDetectionResult-method html
gr html
haplocn.mops html
individualCall-CNVDetectionResult-method
html
individualCall html
iniCall-CNVDetectionResult-method html
iniCall html
integerCopyNumber-CNVDetectionResult-method
html
integerCopyNumber html
localAssessments-CNVDetectionResult-method
html
localAssessments html
makeRobustCNVR html
normalizeChromosomes html
normalizeGenome html
normalizedData-CNVDetectionResult-method
html
normalizedData html
params-CNVDetectionResult-method html
params html
plot html
posteriorProbs-CNVDetectionResult-method
html
posteriorProbs html
referencecn.mops html
sampleNames-CNVDetectionResult-method html
sampleNames html
segment html
segmentation-CNVDetectionResult-method
html
segmentation html
segplot-CNVDetectionResult-method html
segplot html
show html
singlecn.mops html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'cn.mops' ...
** libs
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c R_init_cnmops.c -o R_init_cnmops.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cnmops.cpp -o cnmops.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c segment.cpp -o segment.o
segment.cpp: In function 'SEXPREC* segment(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
segment.cpp:59:20: warning: variable 'globalSd' set but not used [-Wunused-but-set-variable]
double globalMean,globalSd,diff,M2,globalVariance;
^
segment.cpp:60:9: warning: variable 'oldStatistic' set but not used [-Wunused-but-set-variable]
double oldStatistic, meanLeft,meanRight,varLeft,varRight;
^
segment.cpp:61:31: warning: variable 'maxStatistic' set but not used [-Wunused-but-set-variable]
double newStatistic,meanDiff,maxStatistic,DOF,a,b,eps1;
^
segment.cpp:62:40: warning: variable 'maxIdx' set but not used [-Wunused-but-set-variable]
double newPValue, maxPValue,oldPValue,maxIdx;
^
In file included from segment.cpp:10:0:
C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include/Rmath.h:212:15: warning: unused variable 'Rf_beta' [-Wunused-variable]
#define beta Rf_beta
^
segment.cpp:64:9: note: in expansion of macro 'beta'
double beta,nn;
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o cn.mops.dll tmp.def R_init_cnmops.o cnmops.o segment.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/cn.mops.buildbin-libdir/cn.mops/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cn.mops' as cn.mops_1.28.0.zip
* DONE (cn.mops)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'cn.mops' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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cn.mops.Rcheck/examples_i386/cn.mops-Ex.timings
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cn.mops.Rcheck/examples_x64/cn.mops-Ex.timings
|