Guenter Klambauer
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/cn.mops |
| Branch: RELEASE_3_6 |
| Last Commit: 18919e0 |
| Last Changed Date: 2017-10-30 12:39:37 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:10:03 -0400 (Thu, 12 Apr 2018).
| Package 256/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cn.mops 1.24.0 Guenter Klambauer
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: cn.mops |
| Version: 1.24.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.24.0.tar.gz |
| StartedAt: 2018-04-11 22:21:48 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:25:22 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 214.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cn.mops.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings cn.mops_1.24.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/cn.mops.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.24.0’
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
calcFractionalCopyNumbers-CNVDetectionResult-method 15.276 0.028 15.316
referencecn.mops 10.520 0.060 20.771
cn.mops 8.408 0.124 22.868
calcFractionalCopyNumbers 7.924 0.016 7.949
haplocn.mops 1.860 0.096 12.584
getReadCountsFromBAM 1.000 0.032 6.518
getSegmentReadCountsFromBAM 0.228 0.056 6.032
* 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: OK
cn.mops.Rcheck/00install.out
* installing *source* package ‘cn.mops’ ...
** libs
gcc -I/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -c cnmops.cpp -o cnmops.o
g++ -I/home/biocbuild/bbs-3.6-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-3.6-bioc/R/include/Rmath.h:228:15: 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-3.6-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/cn.mops.Rcheck/cn.mops/libs
** R
** data
** inst
** preparing 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 | 15.276 | 0.028 | 15.316 | |
| calcFractionalCopyNumbers | 7.924 | 0.016 | 7.949 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.656 | 0.000 | 0.655 | |
| calcIntegerCopyNumbers | 1.256 | 0.008 | 1.263 | |
| cn.mops | 8.408 | 0.124 | 22.868 | |
| cnvr-CNVDetectionResult-method | 0.216 | 0.000 | 0.218 | |
| cnvr | 0.196 | 0.000 | 0.195 | |
| cnvs-CNVDetectionResult-method | 0.260 | 0.004 | 0.285 | |
| cnvs | 0.268 | 0.004 | 0.273 | |
| exomecn.mops | 4.012 | 0.032 | 4.068 | |
| getReadCountsFromBAM | 1.000 | 0.032 | 6.518 | |
| getSegmentReadCountsFromBAM | 0.228 | 0.056 | 6.032 | |
| gr-CNVDetectionResult-method | 0.252 | 0.028 | 0.282 | |
| gr | 0.292 | 0.008 | 0.300 | |
| haplocn.mops | 1.860 | 0.096 | 12.584 | |
| individualCall-CNVDetectionResult-method | 0.220 | 0.012 | 0.235 | |
| individualCall | 0.216 | 0.000 | 0.220 | |
| iniCall-CNVDetectionResult-method | 0.236 | 0.000 | 0.237 | |
| iniCall | 0.224 | 0.000 | 0.224 | |
| integerCopyNumber-CNVDetectionResult-method | 0.224 | 0.004 | 0.226 | |
| integerCopyNumber | 0.232 | 0.000 | 0.233 | |
| localAssessments-CNVDetectionResult-method | 0.3 | 0.0 | 0.3 | |
| localAssessments | 0.216 | 0.000 | 0.215 | |
| makeRobustCNVR | 0.316 | 0.004 | 0.321 | |
| normalizeChromosomes | 0.208 | 0.012 | 0.220 | |
| normalizeGenome | 0.488 | 0.040 | 0.529 | |
| normalizedData-CNVDetectionResult-method | 0.236 | 0.000 | 0.233 | |
| normalizedData | 0.344 | 0.000 | 0.345 | |
| params-CNVDetectionResult-method | 0.344 | 0.008 | 0.351 | |
| params | 0.324 | 0.008 | 0.330 | |
| posteriorProbs-CNVDetectionResult-method | 0.224 | 0.004 | 0.225 | |
| posteriorProbs | 0.208 | 0.000 | 0.209 | |
| referencecn.mops | 10.520 | 0.060 | 20.771 | |
| sampleNames-CNVDetectionResult-method | 0.260 | 0.020 | 0.281 | |
| sampleNames | 0.232 | 0.024 | 0.259 | |
| segment | 0.024 | 0.000 | 0.023 | |
| segmentation-CNVDetectionResult-method | 0.216 | 0.000 | 0.213 | |
| segmentation | 0.204 | 0.000 | 0.206 | |
| segplot-CNVDetectionResult-method | 0.996 | 0.012 | 1.007 | |
| segplot | 1.212 | 0.004 | 1.214 | |
| singlecn.mops | 0.74 | 0.00 | 0.74 | |