Package: MTseeker

Version: 1.0.6

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_1.0.6.tar.gz

StartedAt: 2019-04-16 01:29:21 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 01:45:06 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 944.8 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_1.0.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MTseeker.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.6’
* 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              340.833  2.353 348.358
MTcircos                 86.664  0.720  88.552
indexMTGenome            26.588  4.700  31.721
MVRangesList-methods     20.256  8.349  14.450
MVRanges-methods         22.773  5.012  20.349
callMT                   12.339  4.006   9.518
injectMTVariants         15.060  0.522  15.812
validMetadata            12.578  0.758  13.526
fixMetadata              11.266  0.989  12.369
MAlignments-methods      10.325  0.545  11.011
MTHGVS                    7.610  0.485   8.286
MAlignmentsList-methods   7.058  0.431   7.547
getMT                     6.538  0.620   7.213
MTcomplex                 6.130  0.492   6.685
filterMTvars              5.622  0.635   6.348
* 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-3.8-bioc/meat/MTseeker.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MTseeker
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MTseeker’ ...
** 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
* DONE (MTseeker)

name	user	system	elapsed
MAlignments-methods	10.325	0.545	11.011
MAlignmentsList-methods	7.058	0.431	7.547
MTHGVS	7.610	0.485	8.286
MTcircos	86.664	0.720	88.552
MTcomplex	6.130	0.492	6.685
MTcoverage	340.833	2.353	348.358
MVRanges-methods	22.773	5.012	20.349
MVRangesList-methods	20.256	8.349	14.450
anno_rCRS	0.025	0.004	0.029
byStrand	2.964	0.581	3.586
callMT	12.339	4.006	9.518
chrominfo.rCRS	0.003	0.003	0.006
filterMT	0.004	0.001	0.004
filterMTvars	5.622	0.635	6.348
fixMetadata	11.266	0.989	12.369
fpFilter_RSRS	0.042	0.003	0.045
fpFilter_Triska	0.007	0.002	0.010
getMT	6.538	0.620	7.213
hg19TorCRS	0.010	0.002	0.011
indexMTGenome	26.588	4.700	31.721
injectMTVariants	15.060	0.522	15.812
mtGenes	0.008	0.002	0.011
mtGenes.rCRS	0.058	0.003	0.071
rCRSeq	0.111	0.005	0.159
s4Methods	1.388	0.009	1.400
validMetadata	12.578	0.758	13.526