Guenter Klambauer
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/cn.mops |
| Branch: RELEASE_3_10 |
| Last Commit: df38eb7 |
| Last Changed Date: 2019-10-29 13:08:24 -0400 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:06:42 -0400 (Wed, 15 Apr 2020).
| Package 316/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cn.mops 1.32.0 Guenter Klambauer
| malbec1 | Linux (Ubuntu 18.04.4 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: 1.32.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings cn.mops_1.32.0.tar.gz |
| StartedAt: 2020-04-15 01:12:21 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:16:07 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 225.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cn.mops.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:cn.mops.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings cn.mops_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/cn.mops.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.32.0’
* 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 12.040 0.120 24.389
cn.mops 6.808 0.256 26.187
calcFractionalCopyNumbers-CNVDetectionResult-method 6.744 0.024 8.150
calcFractionalCopyNumbers 6.484 0.004 7.321
haplocn.mops 1.428 0.204 13.822
getReadCountsFromBAM 0.532 0.068 7.013
getSegmentReadCountsFromBAM 0.380 0.072 6.185
* 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-3.10-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-3.10-bioc/R/bin/R CMD INSTALL cn.mops
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘cn.mops’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.10-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-3.10-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-3.10-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-3.10-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-3.10-bioc/R/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-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 | 0.004 | 0.000 | 0.002 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 6.744 | 0.024 | 8.150 | |
| calcFractionalCopyNumbers | 6.484 | 0.004 | 7.321 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.380 | 0.000 | 0.381 | |
| calcIntegerCopyNumbers | 0.396 | 0.004 | 0.398 | |
| cn.mops | 6.808 | 0.256 | 26.187 | |
| cnvr-CNVDetectionResult-method | 0.304 | 0.016 | 0.319 | |
| cnvr | 0.208 | 0.020 | 0.228 | |
| cnvs-CNVDetectionResult-method | 0.204 | 0.016 | 0.222 | |
| cnvs | 0.200 | 0.004 | 0.204 | |
| exomecn.mops | 3.240 | 0.012 | 3.260 | |
| getReadCountsFromBAM | 0.532 | 0.068 | 7.013 | |
| getSegmentReadCountsFromBAM | 0.380 | 0.072 | 6.185 | |
| gr-CNVDetectionResult-method | 0.336 | 0.008 | 0.348 | |
| gr | 0.300 | 0.032 | 0.330 | |
| haplocn.mops | 1.428 | 0.204 | 13.822 | |
| individualCall-CNVDetectionResult-method | 0.452 | 0.044 | 0.496 | |
| individualCall | 0.364 | 0.028 | 0.391 | |
| iniCall-CNVDetectionResult-method | 0.236 | 0.000 | 0.236 | |
| iniCall | 0.232 | 0.004 | 0.234 | |
| integerCopyNumber-CNVDetectionResult-method | 0.208 | 0.000 | 0.209 | |
| integerCopyNumber | 0.228 | 0.004 | 0.230 | |
| localAssessments-CNVDetectionResult-method | 0.240 | 0.004 | 0.247 | |
| localAssessments | 0.244 | 0.000 | 0.247 | |
| makeRobustCNVR | 0.568 | 0.008 | 0.576 | |
| normalizeChromosomes | 0.248 | 0.000 | 0.246 | |
| normalizeGenome | 0.268 | 0.000 | 0.267 | |
| normalizedData-CNVDetectionResult-method | 0.220 | 0.004 | 0.224 | |
| normalizedData | 0.220 | 0.000 | 0.221 | |
| params-CNVDetectionResult-method | 0.212 | 0.008 | 0.219 | |
| params | 0.212 | 0.008 | 0.220 | |
| posteriorProbs-CNVDetectionResult-method | 0.248 | 0.000 | 0.246 | |
| posteriorProbs | 0.240 | 0.000 | 0.239 | |
| referencecn.mops | 12.040 | 0.120 | 24.389 | |
| sampleNames-CNVDetectionResult-method | 0.340 | 0.004 | 0.361 | |
| sampleNames | 0.196 | 0.028 | 0.224 | |
| segment | 0.028 | 0.008 | 0.033 | |
| segmentation-CNVDetectionResult-method | 0.220 | 0.004 | 0.227 | |
| segmentation | 0.220 | 0.000 | 0.218 | |
| segplot-CNVDetectionResult-method | 1.052 | 0.008 | 1.064 | |
| segplot | 1.504 | 0.004 | 1.538 | |
| singlecn.mops | 1.128 | 0.016 | 1.147 | |