Tim Triche
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/MTseeker |
| Branch: master |
| Last Commit: 44d9481 |
| Last Changed Date: 2018-11-12 12:12:16 -0400 (Mon, 12 Nov 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:52:16 -0400 (Tue, 09 Apr 2019).
| Package 1044/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| MTseeker 1.1.6 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK |
| Package: MTseeker |
| Version: 1.1.6 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MTseeker.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MTseeker_1.1.6.tar.gz |
| StartedAt: 2019-04-09 02:14:26 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 02:28:51 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 865.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MTseeker.Rcheck |
| Warnings: 1 |
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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MTseeker.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MTseeker_1.1.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MTseeker.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.1.6’
* 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 300.785 0.737 303.169
MTcircos 76.473 0.328 76.827
indexMTGenome 35.898 2.978 43.294
MVRanges-methods 19.358 4.819 18.607
MVRangesList-methods 13.318 9.373 11.599
callMT 10.241 3.983 9.047
injectMTVariants 13.817 0.384 14.203
fixMetadata 10.404 0.517 10.939
validMetadata 10.656 0.188 10.854
MAlignments-methods 9.004 0.465 9.604
getMT 7.247 0.060 7.308
MAlignmentsList-methods 6.214 0.469 6.739
filterMTvars 6.105 0.260 6.367
MTHGVS 6.134 0.148 6.284
MTcomplex 5.483 0.241 5.769
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/MTseeker.Rcheck/00check.log’
for details.
MTseeker.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MTseeker ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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 | 9.004 | 0.465 | 9.604 | |
| MAlignmentsList-methods | 6.214 | 0.469 | 6.739 | |
| MTHGVS | 6.134 | 0.148 | 6.284 | |
| MTcircos | 76.473 | 0.328 | 76.827 | |
| MTcomplex | 5.483 | 0.241 | 5.769 | |
| MTcoverage | 300.785 | 0.737 | 303.169 | |
| MVRanges-methods | 19.358 | 4.819 | 18.607 | |
| MVRangesList-methods | 13.318 | 9.373 | 11.599 | |
| anno_rCRS | 0.020 | 0.004 | 0.024 | |
| byStrand | 2.849 | 0.252 | 3.102 | |
| callMT | 10.241 | 3.983 | 9.047 | |
| chrominfo.rCRS | 0.003 | 0.000 | 0.003 | |
| filterMT | 0.004 | 0.000 | 0.004 | |
| filterMTvars | 6.105 | 0.260 | 6.367 | |
| fixMetadata | 10.404 | 0.517 | 10.939 | |
| fpFilter_RSRS | 0.033 | 0.009 | 0.041 | |
| fpFilter_Triska | 0.001 | 0.004 | 0.005 | |
| getMT | 7.247 | 0.060 | 7.308 | |
| hg19TorCRS | 0.013 | 0.000 | 0.013 | |
| indexMTGenome | 35.898 | 2.978 | 43.294 | |
| injectMTVariants | 13.817 | 0.384 | 14.203 | |
| mtGenes | 0.001 | 0.004 | 0.005 | |
| mtGenes.rCRS | 0.033 | 0.004 | 0.037 | |
| rCRSeq | 0.091 | 0.004 | 0.095 | |
| s4Methods | 1.082 | 0.012 | 1.095 | |
| validMetadata | 10.656 | 0.188 | 10.854 | |