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 11:27:15 -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: /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_1.3.0.tar.gz |
| StartedAt: 2019-05-13 02:51:53 -0400 (Mon, 13 May 2019) |
| EndedAt: 2019-05-13 03:07:55 -0400 (Mon, 13 May 2019) |
| EllapsedTime: 962.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MTseeker.Rcheck |
| Warnings: 2 |
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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_1.3.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/MTseeker.Rcheck’
* using R version 3.6.0 (2019-04-26)
* 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 ‘1.3.0’
* 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 332.345 2.183 336.596
MTcircos 90.814 0.847 93.635
indexMTGenome 44.028 6.482 51.352
MVRanges-methods 23.448 4.618 21.296
MVRangesList-methods 19.812 7.645 14.741
callMT 12.811 4.234 10.478
injectMTVariants 13.283 0.533 13.890
MAlignments-methods 12.726 0.543 13.600
fixMetadata 11.033 1.105 12.199
validMetadata 10.944 0.712 11.688
getMT 7.371 0.690 8.251
MAlignmentsList-methods 6.419 0.577 7.046
MTcomplex 6.087 0.468 6.590
MTHGVS 5.477 0.391 5.899
filterMTvars 5.260 0.477 5.763
* 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
‘/Users/biocbuild/bbs-3.10-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 | 12.726 | 0.543 | 13.600 | |
| MAlignmentsList-methods | 6.419 | 0.577 | 7.046 | |
| MTHGVS | 5.477 | 0.391 | 5.899 | |
| MTcircos | 90.814 | 0.847 | 93.635 | |
| MTcomplex | 6.087 | 0.468 | 6.590 | |
| MTcoverage | 332.345 | 2.183 | 336.596 | |
| MVRanges-methods | 23.448 | 4.618 | 21.296 | |
| MVRangesList-methods | 19.812 | 7.645 | 14.741 | |
| anno_rCRS | 0.017 | 0.003 | 0.019 | |
| byStrand | 1.954 | 0.158 | 2.126 | |
| callMT | 12.811 | 4.234 | 10.478 | |
| chrominfo.rCRS | 0.002 | 0.003 | 0.005 | |
| filterMT | 0.004 | 0.001 | 0.004 | |
| filterMTvars | 5.260 | 0.477 | 5.763 | |
| fixMetadata | 11.033 | 1.105 | 12.199 | |
| fpFilter_RSRS | 0.039 | 0.004 | 0.042 | |
| fpFilter_Triska | 0.005 | 0.002 | 0.008 | |
| getMT | 7.371 | 0.690 | 8.251 | |
| hg19TorCRS | 0.014 | 0.003 | 0.018 | |
| indexMTGenome | 44.028 | 6.482 | 51.352 | |
| injectMTVariants | 13.283 | 0.533 | 13.890 | |
| mtGenes | 0.008 | 0.003 | 0.011 | |
| mtGenes.rCRS | 0.042 | 0.003 | 0.044 | |
| rCRSeq | 0.098 | 0.004 | 0.102 | |
| s4Methods | 1.086 | 0.008 | 1.099 | |
| validMetadata | 10.944 | 0.712 | 11.688 | |