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 13:35:09 -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: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cn.mops_1.24.0.tar.gz |
| StartedAt: 2018-04-12 01:52:54 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 01:57:28 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 274.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cn.mops.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings cn.mops_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/cn.mops.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 sizes of PDF files under ‘inst/doc’ ... 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 10.826 0.109 14.206
referencecn.mops 10.284 0.050 21.714
calcFractionalCopyNumbers 9.595 0.047 12.230
cn.mops 8.641 0.153 29.556
haplocn.mops 1.912 0.025 14.977
getReadCountsFromBAM 1.008 0.014 9.503
getSegmentReadCountsFromBAM 0.311 0.007 8.402
* 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
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c R_init_cnmops.c -o R_init_cnmops.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c cnmops.cpp -o cnmops.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c segment.cpp -o segment.o
segment.cpp:64:9: warning: unused variable 'Rf_beta' [-Wunused-variable]
double beta,nn;
^
/Library/Frameworks/R.framework/Resources/include/Rmath.h:228:15: note: expanded from macro 'beta'
#define beta Rf_beta
^
1 warning generated.
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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 | 0.002 | 0.001 | 0.003 | |
| calcFractionalCopyNumbers-CNVDetectionResult-method | 10.826 | 0.109 | 14.206 | |
| calcFractionalCopyNumbers | 9.595 | 0.047 | 12.230 | |
| calcIntegerCopyNumbers-CNVDetectionResult-method | 0.745 | 0.010 | 0.959 | |
| calcIntegerCopyNumbers | 1.189 | 0.008 | 1.510 | |
| cn.mops | 8.641 | 0.153 | 29.556 | |
| cnvr-CNVDetectionResult-method | 0.271 | 0.011 | 0.314 | |
| cnvr | 0.259 | 0.007 | 0.332 | |
| cnvs-CNVDetectionResult-method | 0.269 | 0.008 | 0.351 | |
| cnvs | 0.265 | 0.006 | 0.345 | |
| exomecn.mops | 3.612 | 0.038 | 4.636 | |
| getReadCountsFromBAM | 1.008 | 0.014 | 9.503 | |
| getSegmentReadCountsFromBAM | 0.311 | 0.007 | 8.402 | |
| gr-CNVDetectionResult-method | 0.251 | 0.008 | 0.260 | |
| gr | 0.248 | 0.008 | 0.263 | |
| haplocn.mops | 1.912 | 0.025 | 14.977 | |
| individualCall-CNVDetectionResult-method | 0.282 | 0.009 | 0.319 | |
| individualCall | 0.533 | 0.017 | 0.688 | |
| iniCall-CNVDetectionResult-method | 0.278 | 0.011 | 0.364 | |
| iniCall | 0.273 | 0.015 | 0.362 | |
| integerCopyNumber-CNVDetectionResult-method | 0.292 | 0.016 | 0.406 | |
| integerCopyNumber | 0.285 | 0.014 | 0.401 | |
| localAssessments-CNVDetectionResult-method | 0.277 | 0.015 | 0.385 | |
| localAssessments | 0.288 | 0.016 | 0.392 | |
| makeRobustCNVR | 0.425 | 0.014 | 0.568 | |
| normalizeChromosomes | 0.324 | 0.029 | 0.457 | |
| normalizeGenome | 0.323 | 0.018 | 0.452 | |
| normalizedData-CNVDetectionResult-method | 0.274 | 0.010 | 0.350 | |
| normalizedData | 0.285 | 0.012 | 0.386 | |
| params-CNVDetectionResult-method | 0.238 | 0.017 | 0.262 | |
| params | 0.262 | 0.017 | 0.286 | |
| posteriorProbs-CNVDetectionResult-method | 0.247 | 0.011 | 0.270 | |
| posteriorProbs | 0.247 | 0.010 | 0.261 | |
| referencecn.mops | 10.284 | 0.050 | 21.714 | |
| sampleNames-CNVDetectionResult-method | 0.242 | 0.011 | 0.275 | |
| sampleNames | 0.248 | 0.010 | 0.262 | |
| segment | 0.026 | 0.000 | 0.030 | |
| segmentation-CNVDetectionResult-method | 0.270 | 0.012 | 0.288 | |
| segmentation | 0.279 | 0.012 | 0.292 | |
| segplot-CNVDetectionResult-method | 1.237 | 0.014 | 1.263 | |
| segplot | 1.563 | 0.018 | 1.599 | |
| singlecn.mops | 0.954 | 0.016 | 0.977 | |