Guenter Klambauer
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/cn.mops |
| Branch: RELEASE_3_7 |
| Last Commit: 2f07225 |
| Last Changed Date: 2018-04-30 10:35:22 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:24:03 -0400 (Wed, 17 Oct 2018).
| Package 269/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cn.mops 1.26.0 Guenter Klambauer
| 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: cn.mops |
| Version: 1.26.0 |
| Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings cn.mops_1.26.0.tar.gz |
| StartedAt: 2018-10-15 23:20:08 -0400 (Mon, 15 Oct 2018) |
| EndedAt: 2018-10-15 23:23:16 -0400 (Mon, 15 Oct 2018) |
| EllapsedTime: 188.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cn.mops.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings cn.mops_1.26.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/cn.mops.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.26.0’
* 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
calcFractionalCopyNumbers-CNVDetectionResult-method 13.348 0.024 13.385
referencecn.mops 11.660 0.072 20.822
calcFractionalCopyNumbers 9.464 0.000 9.489
cn.mops 7.360 0.164 21.047
haplocn.mops 1.480 0.088 10.965
getReadCountsFromBAM 0.460 0.040 5.734
getSegmentReadCountsFromBAM 0.244 0.064 5.854
* 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-3.7-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-3.7-bioc/R/bin/R CMD INSTALL cn.mops
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘cn.mops’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cnmops.cpp -o cnmops.o
g++ -I"/home/biocbuild/bbs-3.7-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-3.7-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-3.7-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-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 | 0.001 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 13.348 | 0.024 | 13.385 | |
| calcFractionalCopyNumbers | 9.464 | 0.000 | 9.489 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.352 | 0.008 | 0.363 | |
| calcIntegerCopyNumbers | 0.296 | 0.004 | 0.301 | |
| cn.mops | 7.360 | 0.164 | 21.047 | |
| cnvr-CNVDetectionResult-method | 0.304 | 0.004 | 0.307 | |
| cnvr | 0.668 | 0.060 | 0.731 | |
| cnvs-CNVDetectionResult-method | 0.280 | 0.004 | 0.288 | |
| cnvs | 0.220 | 0.004 | 0.225 | |
| exomecn.mops | 3.324 | 0.008 | 3.333 | |
| getReadCountsFromBAM | 0.460 | 0.040 | 5.734 | |
| getSegmentReadCountsFromBAM | 0.244 | 0.064 | 5.854 | |
| gr-CNVDetectionResult-method | 0.332 | 0.016 | 0.349 | |
| gr | 0.328 | 0.008 | 0.333 | |
| haplocn.mops | 1.480 | 0.088 | 10.965 | |
| individualCall-CNVDetectionResult-method | 0.348 | 0.020 | 0.365 | |
| individualCall | 0.204 | 0.000 | 0.207 | |
| iniCall-CNVDetectionResult-method | 0.192 | 0.004 | 0.197 | |
| iniCall | 0.280 | 0.000 | 0.285 | |
| integerCopyNumber-CNVDetectionResult-method | 0.204 | 0.000 | 0.207 | |
| integerCopyNumber | 0.216 | 0.000 | 0.212 | |
| localAssessments-CNVDetectionResult-method | 0.188 | 0.004 | 0.195 | |
| localAssessments | 0.200 | 0.000 | 0.203 | |
| makeRobustCNVR | 0.356 | 0.008 | 0.366 | |
| normalizeChromosomes | 0.34 | 0.02 | 0.36 | |
| normalizeGenome | 0.408 | 0.000 | 0.410 | |
| normalizedData-CNVDetectionResult-method | 0.276 | 0.000 | 0.278 | |
| normalizedData | 0.204 | 0.004 | 0.210 | |
| params-CNVDetectionResult-method | 0.212 | 0.012 | 0.222 | |
| params | 0.336 | 0.004 | 0.337 | |
| posteriorProbs-CNVDetectionResult-method | 0.272 | 0.004 | 0.278 | |
| posteriorProbs | 0.208 | 0.004 | 0.211 | |
| referencecn.mops | 11.660 | 0.072 | 20.822 | |
| sampleNames-CNVDetectionResult-method | 0.220 | 0.024 | 0.247 | |
| sampleNames | 0.180 | 0.004 | 0.187 | |
| segment | 0.024 | 0.000 | 0.022 | |
| segmentation-CNVDetectionResult-method | 0.188 | 0.004 | 0.190 | |
| segmentation | 0.200 | 0.000 | 0.202 | |
| segplot-CNVDetectionResult-method | 0.864 | 0.008 | 0.873 | |
| segplot | 0.864 | 0.004 | 0.868 | |
| singlecn.mops | 1.140 | 0.012 | 1.152 | |