Tim Triche
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/MTseeker |
| Branch: RELEASE_3_9 |
| Last Commit: 51756bd |
| Last Changed Date: 2019-05-02 11:54:13 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 13:03:48 -0400 (Wed, 16 Oct 2019).
| Package 1062/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MTseeker 1.2.0 Tim Triche
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | ERROR | ERROR | skipped | skipped | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK | |
| Package: MTseeker |
| Version: 1.2.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MTseeker.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MTseeker_1.2.0.tar.gz |
| StartedAt: 2019-10-16 04:55:55 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:18:07 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 1332.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MTseeker.Rcheck |
| Warnings: 1 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MTseeker.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MTseeker_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/MTseeker.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MTseeker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MTseeker’ version ‘1.2.0’
* package encoding: UTF-8
* 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 ‘MTseeker’ 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 ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::labeledLine’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.colorCode: no visible binding for global variable ‘mtAnno’
MAlignmentsList: no visible binding for global variable ‘reads’
MAlignmentsList: no visible binding for global variable ‘genomeSize’
MTcircos: no visible binding for global variable ‘mtAnno’
MTcomplex: no visible binding for global variable ‘mtAnno’
byStrand: no visible binding for global variable ‘mtAnno’
callMT: no visible global function definition for ‘mcmapply’
filterMT: no visible binding for global variable ‘mtCovg’
filterMT: no visible binding for global variable ‘fpFilter_Triska’
filterMTvars: no visible binding for global variable ‘fpFilter_Triska’
filterMTvars: no visible binding for global variable ‘VAF’
filterMTvars: no visible binding for global variable ‘PASS’
getMT: no visible global function definition for ‘mclapply’
injectMTVariants: no visible binding for global variable ‘VAF’
injectMTVariants: no visible binding for global variable ‘rCRSeq’
plotMTCoverage: no visible binding for global variable ‘mtAnno’
plotStrandedMTCoverage: no visible binding for global variable ‘mtAnno’
annotation,MVRanges: no visible binding for global variable ‘mtAnno’
consensusString,MVRanges: no visible binding for global variable
‘rCRSeq’
encoding,MVRanges: no visible binding for global variable ‘region’
filt,MVRangesList: no visible binding for global variable ‘PASS’
genes,MVRanges: no visible binding for global variable ‘region’
genes,MVRangesList: no visible binding for global variable ‘region’
getAnnotations,MVRanges: no visible binding for global variable
‘mtAnno’
locateVariants,MVRanges-missing-missing: no visible binding for global
variable ‘mtAnno’
locateVariants,MVRanges-missing-missing: no visible binding for global
variable ‘region’
summarizeVariants,MVRanges-missing-missing : getImpact: no visible
binding for global variable ‘Start’
summarizeVariants,MVRanges-missing-missing : getImpact: no visible
binding for global variable ‘Ref’
summarizeVariants,MVRanges-missing-missing : getImpact: no visible
binding for global variable ‘Alt’
summarizeVariants,MVRanges-missing-missing : getImpact: no visible
binding for global variable ‘AA_ref’
summarizeVariants,MVRanges-missing-missing : getImpact: no visible
binding for global variable ‘AA_position’
summarizeVariants,MVRanges-missing-missing : getImpact: no visible
binding for global variable ‘AA_alt’
summarizeVariants,MVRanges-missing-missing : getImpact: no visible
binding for global variable ‘Gene_symbol’
summarizeVariants,MVRanges-missing-missing : getImpact: no visible
binding for global variable ‘protein’
summarizeVariants,MVRangesList-missing-missing : getRangedImpact: no
visible binding for global variable ‘Start’
summarizeVariants,MVRangesList-missing-missing : getRangedImpact: no
visible binding for global variable ‘Ref’
summarizeVariants,MVRangesList-missing-missing : getRangedImpact: no
visible binding for global variable ‘Alt’
summarizeVariants,MVRangesList-missing-missing : getRangedImpact: no
visible binding for global variable ‘AA_ref’
summarizeVariants,MVRangesList-missing-missing : getRangedImpact: no
visible binding for global variable ‘AA_position’
summarizeVariants,MVRangesList-missing-missing : getRangedImpact: no
visible binding for global variable ‘AA_alt’
summarizeVariants,MVRangesList-missing-missing : getRangedImpact: no
visible binding for global variable ‘Gene_symbol’
Undefined global functions or variables:
AA_alt AA_position AA_ref Alt Gene_symbol PASS Ref Start VAF
fpFilter_Triska genomeSize mclapply mcmapply mtAnno mtCovg protein
rCRSeq reads region
* 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 ... WARNING
'library' or 'require' call not declared from: ‘GmapGenome.Hsapiens.rCRS’
* 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 Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
MTcoverage 499.159 5.360 512.033
MTcircos 107.742 1.515 109.896
indexMTGenome 57.884 11.807 70.966
MVRangesList-methods 26.491 14.950 21.599
MVRanges-methods 29.912 8.305 27.672
callMT 15.657 7.568 13.585
MAlignments-methods 15.908 1.108 17.187
injectMTVariants 15.887 0.908 16.796
fixMetadata 12.303 2.349 14.653
validMetadata 12.977 1.371 14.351
MAlignmentsList-methods 7.478 1.084 8.597
getMT 7.347 1.024 8.371
MTcomplex 7.228 0.793 8.814
MTHGVS 6.577 0.730 7.308
filterMTvars 5.860 0.929 6.790
* 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 WARNING, 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-bioc/meat/MTseeker.Rcheck/00check.log’
for details.
MTseeker.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MTseeker ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘MTseeker’ ... ** using staged installation ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (MTseeker)
MTseeker.Rcheck/MTseeker-Ex.timings
| name | user | system | elapsed | |
| MAlignments-methods | 15.908 | 1.108 | 17.187 | |
| MAlignmentsList-methods | 7.478 | 1.084 | 8.597 | |
| MTHGVS | 6.577 | 0.730 | 7.308 | |
| MTcircos | 107.742 | 1.515 | 109.896 | |
| MTcomplex | 7.228 | 0.793 | 8.814 | |
| MTcoverage | 499.159 | 5.360 | 512.033 | |
| MVRanges-methods | 29.912 | 8.305 | 27.672 | |
| MVRangesList-methods | 26.491 | 14.950 | 21.599 | |
| anno_rCRS | 0.025 | 0.010 | 0.036 | |
| byStrand | 2.544 | 0.321 | 2.866 | |
| callMT | 15.657 | 7.568 | 13.585 | |
| chrominfo.rCRS | 0.003 | 0.004 | 0.007 | |
| filterMT | 0.005 | 0.002 | 0.007 | |
| filterMTvars | 5.860 | 0.929 | 6.790 | |
| fixMetadata | 12.303 | 2.349 | 14.653 | |
| fpFilter_RSRS | 0.049 | 0.006 | 0.055 | |
| fpFilter_Triska | 0.007 | 0.005 | 0.012 | |
| getMT | 7.347 | 1.024 | 8.371 | |
| hg19TorCRS | 0.012 | 0.004 | 0.015 | |
| indexMTGenome | 57.884 | 11.807 | 70.966 | |
| injectMTVariants | 15.887 | 0.908 | 16.796 | |
| mtGenes | 0.009 | 0.005 | 0.015 | |
| mtGenes.rCRS | 0.067 | 0.006 | 0.073 | |
| rCRSeq | 0.146 | 0.011 | 0.158 | |
| s4Methods | 1.519 | 0.012 | 1.533 | |
| validMetadata | 12.977 | 1.371 | 14.351 | |