Guenter Klambauer
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/cn.mops |
| Branch: RELEASE_3_9 |
| Last Commit: a17073a |
| Last Changed Date: 2019-05-02 11:53:33 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:00:45 -0400 (Wed, 16 Oct 2019).
| Package 300/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cn.mops 1.30.0 Guenter Klambauer
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: cn.mops |
| Version: 1.30.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cn.mops_1.30.0.tar.gz |
| StartedAt: 2019-10-16 00:38:08 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 00:42:05 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 237.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cn.mops.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings cn.mops_1.30.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/cn.mops.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.30.0’
* 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 15.243 0.113 27.098
calcFractionalCopyNumbers 10.704 0.000 10.718
calcFractionalCopyNumbers-CNVDetectionResult-method 10.552 0.019 10.605
cn.mops 8.335 0.204 24.410
haplocn.mops 1.393 0.137 13.527
getReadCountsFromBAM 0.420 0.045 6.178
getSegmentReadCountsFromBAM 0.347 0.092 6.265
* 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-3.9-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-3.9-bioc/R/bin/R CMD INSTALL cn.mops
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c R_init_cnmops.c -o R_init_cnmops.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cnmops.cpp -o cnmops.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-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-3.9-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++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-cn.mops/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cn.mops)
cn.mops.Rcheck/cn.mops-Ex.timings
| name | user | system | elapsed | |
| CNVDetectionResult | 0.002 | 0.000 | 0.002 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 10.552 | 0.019 | 10.605 | |
| calcFractionalCopyNumbers | 10.704 | 0.000 | 10.718 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.856 | 0.000 | 0.858 | |
| calcIntegerCopyNumbers | 0.279 | 0.004 | 0.284 | |
| cn.mops | 8.335 | 0.204 | 24.410 | |
| cnvr-CNVDetectionResult-method | 0.269 | 0.012 | 0.281 | |
| cnvr | 0.634 | 0.048 | 0.686 | |
| cnvs-CNVDetectionResult-method | 0.253 | 0.008 | 0.261 | |
| cnvs | 0.272 | 0.000 | 0.273 | |
| exomecn.mops | 4.023 | 0.000 | 4.028 | |
| getReadCountsFromBAM | 0.420 | 0.045 | 6.178 | |
| getSegmentReadCountsFromBAM | 0.347 | 0.092 | 6.265 | |
| gr-CNVDetectionResult-method | 0.297 | 0.008 | 0.305 | |
| gr | 0.282 | 0.004 | 0.286 | |
| haplocn.mops | 1.393 | 0.137 | 13.527 | |
| individualCall-CNVDetectionResult-method | 0.307 | 0.016 | 0.323 | |
| individualCall | 0.293 | 0.012 | 0.306 | |
| iniCall-CNVDetectionResult-method | 0.267 | 0.000 | 0.267 | |
| iniCall | 0.269 | 0.000 | 0.269 | |
| integerCopyNumber-CNVDetectionResult-method | 0.299 | 0.000 | 0.299 | |
| integerCopyNumber | 0.268 | 0.004 | 0.273 | |
| localAssessments-CNVDetectionResult-method | 0.289 | 0.008 | 0.297 | |
| localAssessments | 0.264 | 0.004 | 0.268 | |
| makeRobustCNVR | 0.489 | 0.000 | 0.489 | |
| normalizeChromosomes | 0.265 | 0.008 | 0.278 | |
| normalizeGenome | 0.261 | 0.000 | 0.260 | |
| normalizedData-CNVDetectionResult-method | 0.264 | 0.000 | 0.264 | |
| normalizedData | 0.285 | 0.004 | 0.289 | |
| params-CNVDetectionResult-method | 0.267 | 0.008 | 0.275 | |
| params | 0.269 | 0.004 | 0.273 | |
| posteriorProbs-CNVDetectionResult-method | 0.254 | 0.000 | 0.253 | |
| posteriorProbs | 0.251 | 0.008 | 0.260 | |
| referencecn.mops | 15.243 | 0.113 | 27.098 | |
| sampleNames-CNVDetectionResult-method | 0.265 | 0.016 | 0.281 | |
| sampleNames | 0.278 | 0.012 | 0.290 | |
| segment | 0.024 | 0.000 | 0.024 | |
| segmentation-CNVDetectionResult-method | 0.27 | 0.00 | 0.27 | |
| segmentation | 0.266 | 0.003 | 0.269 | |
| segplot-CNVDetectionResult-method | 1.173 | 0.000 | 1.172 | |
| segplot | 1.184 | 0.016 | 1.208 | |
| singlecn.mops | 1.144 | 0.004 | 1.148 | |