Tim Triche
| Snapshot Date: 2019-05-12 17:00:25 -0400 (Sun, 12 May 2019) |
| URL: https://git.bioconductor.org/packages/MTseeker |
| Branch: master |
| Last Commit: 8678848 |
| Last Changed Date: 2019-05-02 12:16:10 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2019-05-13 11:19:57 -0400 (Mon, 13 May 2019).
| Package 1056/1728 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MTseeker 1.3.0 Tim Triche
| malbec1 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: MTseeker |
| Version: 1.3.0 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MTseeker.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MTseeker_1.3.0.tar.gz |
| StartedAt: 2019-05-13 03:35:56 -0400 (Mon, 13 May 2019) |
| EndedAt: 2019-05-13 03:50:36 -0400 (Mon, 13 May 2019) |
| EllapsedTime: 880.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MTseeker.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:MTseeker.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings MTseeker_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/MTseeker.Rcheck’
* using R version 3.6.0 (2019-04-26)
* using platform: x86_64-pc-linux-gnu (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 ‘1.3.0’
* 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 ... WARNING
Found the following significant warnings:
Warning: 'GenomicRangesList' is deprecated.
Warning: 'GenomicRangesList' is deprecated.
Warning: 'GenomicRangesList' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
user system elapsed
MTcoverage 300.468 0.656 303.549
MTcircos 75.380 0.216 75.845
indexMTGenome 43.988 2.788 52.405
MVRanges-methods 18.756 4.620 18.087
MVRangesList-methods 14.188 8.528 13.059
callMT 9.916 4.480 8.936
MAlignments-methods 12.344 0.788 13.358
validMetadata 12.240 0.172 12.464
fixMetadata 11.836 0.316 12.198
injectMTVariants 11.080 0.356 11.449
MAlignmentsList-methods 6.412 0.332 6.780
MTHGVS 6.120 0.244 6.381
getMT 6.296 0.048 6.359
MTcomplex 5.564 0.260 5.846
filterMTvars 5.208 0.136 5.351
* 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: 2 WARNINGs, 2 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/MTseeker.Rcheck/00check.log’
for details.
MTseeker.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL MTseeker ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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 | 12.344 | 0.788 | 13.358 | |
| MAlignmentsList-methods | 6.412 | 0.332 | 6.780 | |
| MTHGVS | 6.120 | 0.244 | 6.381 | |
| MTcircos | 75.380 | 0.216 | 75.845 | |
| MTcomplex | 5.564 | 0.260 | 5.846 | |
| MTcoverage | 300.468 | 0.656 | 303.549 | |
| MVRanges-methods | 18.756 | 4.620 | 18.087 | |
| MVRangesList-methods | 14.188 | 8.528 | 13.059 | |
| anno_rCRS | 0.008 | 0.004 | 0.013 | |
| byStrand | 1.564 | 0.084 | 1.649 | |
| callMT | 9.916 | 4.480 | 8.936 | |
| chrominfo.rCRS | 0.000 | 0.000 | 0.002 | |
| filterMT | 0.004 | 0.000 | 0.003 | |
| filterMTvars | 5.208 | 0.136 | 5.351 | |
| fixMetadata | 11.836 | 0.316 | 12.198 | |
| fpFilter_RSRS | 0.016 | 0.008 | 0.023 | |
| fpFilter_Triska | 0.004 | 0.000 | 0.004 | |
| getMT | 6.296 | 0.048 | 6.359 | |
| hg19TorCRS | 0.012 | 0.000 | 0.014 | |
| indexMTGenome | 43.988 | 2.788 | 52.405 | |
| injectMTVariants | 11.080 | 0.356 | 11.449 | |
| mtGenes | 0.000 | 0.004 | 0.004 | |
| mtGenes.rCRS | 0.032 | 0.000 | 0.032 | |
| rCRSeq | 0.072 | 0.000 | 0.069 | |
| s4Methods | 0.988 | 0.000 | 0.992 | |
| validMetadata | 12.240 | 0.172 | 12.464 | |