Guenter Klambauer
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 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 2019-04-16 11:49:27 -0400 (Tue, 16 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 ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: cn.mops |
| Version: 1.28.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings cn.mops_1.28.0.tar.gz |
| StartedAt: 2019-04-15 23:00:22 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:04:12 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 229.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cn.mops.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings cn.mops_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/cn.mops.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 ... 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 for sufficient/correct file permissions ... 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
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
referencecn.mops 13.452 0.104 24.248
calcFractionalCopyNumbers 11.044 0.008 11.060
calcFractionalCopyNumbers-CNVDetectionResult-method 10.784 0.008 10.817
cn.mops 9.920 0.168 25.056
haplocn.mops 1.384 0.128 12.790
getReadCountsFromBAM 0.800 0.028 6.590
getSegmentReadCountsFromBAM 0.396 0.068 6.145
* 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
‘/home/biocbuild/bbs-3.8-bioc/meat/cn.mops.Rcheck/00check.log’
for details.
cn.mops.Rcheck/00install.out
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### Running command:
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### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL cn.mops
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘cn.mops’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_cnmops.c -o R_init_cnmops.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cnmops.cpp -o cnmops.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -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:
/home/biocbuild/bbs-3.8-bioc/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;
^
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/cn.mops/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.mops)
cn.mops.Rcheck/cn.mops-Ex.timings
| name | user | system | elapsed | |
| CNVDetectionResult | 0.000 | 0.000 | 0.002 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 10.784 | 0.008 | 10.817 | |
| calcFractionalCopyNumbers | 11.044 | 0.008 | 11.060 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.536 | 0.008 | 0.543 | |
| calcIntegerCopyNumbers | 0.456 | 0.000 | 0.453 | |
| cn.mops | 9.920 | 0.168 | 25.056 | |
| cnvr-CNVDetectionResult-method | 0.316 | 0.028 | 0.344 | |
| cnvr | 0.188 | 0.008 | 0.196 | |
| cnvs-CNVDetectionResult-method | 0.520 | 0.028 | 0.550 | |
| cnvs | 0.184 | 0.004 | 0.192 | |
| exomecn.mops | 2.856 | 0.000 | 2.857 | |
| getReadCountsFromBAM | 0.800 | 0.028 | 6.590 | |
| getSegmentReadCountsFromBAM | 0.396 | 0.068 | 6.145 | |
| gr-CNVDetectionResult-method | 0.328 | 0.032 | 0.365 | |
| gr | 0.348 | 0.004 | 0.354 | |
| haplocn.mops | 1.384 | 0.128 | 12.790 | |
| individualCall-CNVDetectionResult-method | 0.336 | 0.012 | 0.349 | |
| individualCall | 0.332 | 0.008 | 0.342 | |
| iniCall-CNVDetectionResult-method | 0.344 | 0.000 | 0.342 | |
| iniCall | 0.300 | 0.004 | 0.306 | |
| integerCopyNumber-CNVDetectionResult-method | 0.272 | 0.008 | 0.281 | |
| integerCopyNumber | 0.336 | 0.004 | 0.339 | |
| localAssessments-CNVDetectionResult-method | 0.280 | 0.004 | 0.285 | |
| localAssessments | 0.196 | 0.000 | 0.194 | |
| makeRobustCNVR | 0.280 | 0.004 | 0.283 | |
| normalizeChromosomes | 0.596 | 0.020 | 0.619 | |
| normalizeGenome | 0.608 | 0.000 | 0.608 | |
| normalizedData-CNVDetectionResult-method | 0.208 | 0.000 | 0.208 | |
| normalizedData | 0.308 | 0.008 | 0.316 | |
| params-CNVDetectionResult-method | 0.296 | 0.004 | 0.301 | |
| params | 0.304 | 0.008 | 0.312 | |
| posteriorProbs-CNVDetectionResult-method | 0.312 | 0.000 | 0.315 | |
| posteriorProbs | 0.252 | 0.000 | 0.256 | |
| referencecn.mops | 13.452 | 0.104 | 24.248 | |
| sampleNames-CNVDetectionResult-method | 0.244 | 0.020 | 0.268 | |
| sampleNames | 0.304 | 0.008 | 0.313 | |
| segment | 0.028 | 0.000 | 0.029 | |
| segmentation-CNVDetectionResult-method | 0.320 | 0.000 | 0.322 | |
| segmentation | 0.332 | 0.000 | 0.336 | |
| segplot-CNVDetectionResult-method | 0.956 | 0.008 | 0.969 | |
| segplot | 0.892 | 0.000 | 0.893 | |
| singlecn.mops | 0.712 | 0.004 | 0.715 | |