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 12:16:52 -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: /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_1.2.0.tar.gz |
| StartedAt: 2019-10-16 03:24:48 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 03:39:43 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 895.0 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_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MTseeker.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.2.0’
* 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 326.135 0.544 328.268
MTcircos 74.932 0.144 75.107
indexMTGenome 43.813 3.183 50.144
MVRanges-methods 19.645 4.757 18.651
MVRangesList-methods 14.934 8.955 12.880
injectMTVariants 15.070 0.516 15.603
callMT 10.430 4.612 9.640
MAlignments-methods 14.219 0.760 15.128
fixMetadata 11.651 0.316 11.967
validMetadata 9.691 0.215 9.915
MAlignmentsList-methods 5.894 0.315 6.251
getMT 5.895 0.072 5.967
MTHGVS 5.160 0.248 5.410
* 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 | 14.219 | 0.760 | 15.128 | |
| MAlignmentsList-methods | 5.894 | 0.315 | 6.251 | |
| MTHGVS | 5.160 | 0.248 | 5.410 | |
| MTcircos | 74.932 | 0.144 | 75.107 | |
| MTcomplex | 4.599 | 0.262 | 4.980 | |
| MTcoverage | 326.135 | 0.544 | 328.268 | |
| MVRanges-methods | 19.645 | 4.757 | 18.651 | |
| MVRangesList-methods | 14.934 | 8.955 | 12.880 | |
| anno_rCRS | 0.019 | 0.000 | 0.020 | |
| byStrand | 1.599 | 0.056 | 1.655 | |
| callMT | 10.430 | 4.612 | 9.640 | |
| chrominfo.rCRS | 0.001 | 0.000 | 0.002 | |
| filterMT | 0.002 | 0.000 | 0.002 | |
| filterMTvars | 3.614 | 0.120 | 3.734 | |
| fixMetadata | 11.651 | 0.316 | 11.967 | |
| fpFilter_RSRS | 0.036 | 0.000 | 0.036 | |
| fpFilter_Triska | 0.006 | 0.000 | 0.006 | |
| getMT | 5.895 | 0.072 | 5.967 | |
| hg19TorCRS | 0.009 | 0.004 | 0.013 | |
| indexMTGenome | 43.813 | 3.183 | 50.144 | |
| injectMTVariants | 15.070 | 0.516 | 15.603 | |
| mtGenes | 0.004 | 0.004 | 0.008 | |
| mtGenes.rCRS | 0.055 | 0.004 | 0.060 | |
| rCRSeq | 0.096 | 0.000 | 0.096 | |
| s4Methods | 0.781 | 0.000 | 0.782 | |
| validMetadata | 9.691 | 0.215 | 9.915 | |