Package: MAGeCKFlute

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MAGeCKFlute.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MAGeCKFlute_1.7.0.tar.gz

StartedAt: 2019-12-24 05:29:27 -0500 (Tue, 24 Dec 2019)

EndedAt: 2019-12-24 05:40:18 -0500 (Tue, 24 Dec 2019)

EllapsedTime: 651.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MAGeCKFlute.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:MAGeCKFlute.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MAGeCKFlute_1.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/MAGeCKFlute.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAGeCKFlute/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAGeCKFlute’ version ‘1.7.0’
* 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 ... NOTE
Found the following non-portable file paths:
  MAGeCKFlute/vignettes/MAGeCKFlute_cache/html/CheckCountSummary_d66bfb769e5891687ce7610008b8f5fb.RData
  MAGeCKFlute/vignettes/MAGeCKFlute_cache/html/EstimateCellCycle_830b2fefb5d3bb8faf97d373184d55a8.RData

Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MAGeCKFlute’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘DOSE::.__C__compareClusterResult’ by ‘clusterProfiler::.__C__compareClusterResult’ when loading ‘MAGeCKFlute’
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/MAGeCKFlute.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data      5.3Mb
    doc       1.1Mb
    extdata   9.5Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File ‘MAGeCKFlute/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage(paste(strwrap(disclaimer, 80), collapse = "\n"))

See section ‘Good practice’ in '?.onAttach'.

BatchRemove: no visible binding for global variable ‘PC1’
BatchRemove: no visible binding for global variable ‘PC2’
BatchRemove: no visible binding for global variable ‘shape’
CellCycleView: no visible binding for global variable ‘x’
CellCycleView: no visible binding for global variable ‘y’
DensityDiffView: no visible binding for global variable ‘Diff’
DensityDiffView: no visible binding for global variable ‘..density..’
DensityDiffView: no visible binding for global variable ‘r’
DensityView: no visible binding for global variable ‘value’
DensityView: no visible binding for global variable ‘variable’
EnrichedFilter: no visible binding for global variable ‘max_value’
EnrichedGeneView: no visible binding for global variable ‘Gene’
EnrichedGeneView: no visible binding for global variable ‘Term’
EnrichedGeneView: no visible binding for global variable ‘Size’
EnrichedGeneView: no visible binding for global variable ‘GeneScore’
EnrichedView: no visible binding for global variable ‘Description’
EnrichedView: no visible binding for global variable ‘size’
FluteMLE: no visible binding for global variable ‘Zuber_Essential’
KeggPathwayView: no visible global function definition for ‘keggConv’
KeggPathwayView: no visible binding for global variable ‘rn.list’
KeggPathwayView: no visible global function definition for
  ‘parseKGML2Graph2’
MapRatesView: no visible binding for global variable ‘count’
MapRatesView: no visible binding for global variable ‘category’
MapRatesView: no visible binding for global variable ‘pos’
MapRatesView: no visible binding for global variable ‘percent’
NormalizeBeta: no visible binding for global variable ‘Zuber_Essential’
RankView: no visible binding for global variable ‘Rank’
RankView: no visible binding for global variable ‘group’
RankView: no visible binding for global variable ‘Gene’
ScatterView: no visible binding for global variable ‘Control’
ScatterView: no visible binding for global variable ‘Treatment’
ScatterView: no visible binding for global variable ‘group’
Selector: no visible binding for global variable ‘GeneNum’
Selector: no visible binding for global variable ‘x’
Selector: no visible binding for global variable ‘y’
SquareView: no visible binding for global variable ‘x’
SquareView: no visible binding for global variable ‘y’
SquareView: no visible binding for global variable ‘group’
SquareView: no visible binding for global variable ‘Gene’
ViolinView: no visible binding for global variable ‘variable’
ViolinView: no visible binding for global variable ‘value’
VolcanoView: no visible binding for global variable ‘group’
VolcanoView: no visible binding for global variable ‘color’
sgRankView: no visible global function definition for ‘.’
sgRankView: no visible binding for global variable ‘LFC’
sgRankView: no visible binding for global variable ‘Gene’
sgRankView: no visible binding for global variable ‘x’
sgRankView: no visible binding for global variable ‘y’
sgRankView: no visible binding for global variable ‘value’
sgRankView: no visible binding for global variable ‘id’
sgRankView: no visible binding for global variable ‘yend’
Undefined global functions or variables:
  . ..density.. Control Description Diff Gene GeneNum GeneScore LFC PC1
  PC2 Rank Size Term Treatment Zuber_Essential category color count
  group id keggConv max_value parseKGML2Graph2 percent pos r rn.list
  shape size value variable x y yend
* 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 ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
gsGetter         38.764  1.219  39.985
enrich.ORT       35.381  0.631  36.019
EnrichAnalyzer   31.842  1.576  33.395
MAView           33.098  0.200  33.303
EnrichedGeneView 26.389  0.991  26.574
EnrichedFilter   26.228  0.931  25.773
arrangePathview  21.984  1.261  25.236
enrich.HGT       21.188  0.411  21.598
TransGeneID      14.667  0.350  15.017
getOrg           14.264  0.225  14.491
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/MAGeCKFlute.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 MAGeCKFlute
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘MAGeCKFlute’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘DOSE::.__C__compareClusterResult’ by ‘clusterProfiler::.__C__compareClusterResult’ when loading ‘MAGeCKFlute’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘DOSE::.__C__compareClusterResult’ by ‘clusterProfiler::.__C__compareClusterResult’ when loading ‘MAGeCKFlute’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘DOSE::.__C__compareClusterResult’ by ‘clusterProfiler::.__C__compareClusterResult’ when loading ‘MAGeCKFlute’
** testing if installed package keeps a record of temporary installation path
* DONE (MAGeCKFlute)

name	user	system	elapsed
BatchRemove	1.947	0.049	1.997
CellCycleView	0.879	0.109	0.989
CutoffCalling	0.003	0.000	0.004
DensityDiffView	1.193	0.065	1.261
DensityView	0.861	0.057	0.918
EnrichAB	0.067	0.016	0.082
EnrichAnalyzer	31.842	1.576	33.395
EnrichSquare	0.319	0.197	0.154
EnrichedFilter	26.228	0.931	25.773
EnrichedGeneView	26.389	0.991	26.574
EnrichedView	0.000	0.000	0.001
FluteMLE	0.002	0.002	0.005
FluteRRA	0.004	0.004	0.009
HeatmapView	0.116	0.011	0.127
IdentBarView	0.263	0.003	0.266
KeggPathwayView	0.032	0.011	0.042
MAView	33.098	0.200	33.303
MapRatesView	0.619	0.009	0.630
NormalizeBeta	0.324	0.033	0.358
RankView	2.366	0.125	2.491
ReadBeta	0.035	0.011	0.046
ReadRRA	0.984	0.022	1.006
ReadsgRRA	0.521	0.043	0.565
ScatterView	1.059	0.066	1.127
Selector	0.274	0.008	0.283
SquareView	1.941	0.135	2.075
TransGeneID	14.667	0.350	15.017
ViolinView	2.705	0.237	2.943
VolcanoView	2.966	0.176	3.143
arrangePathview	21.984	1.261	25.236
countsummary	0.009	0.003	0.012
enrich.GSE	0.015	0.001	0.016
enrich.HGT	21.188	0.411	21.598
enrich.ORT	35.381	0.631	36.019
getOrg	14.264	0.225	14.491
gsGetter	38.764	1.219	39.985
mle.gene_summary	0.041	0.013	0.055
normalize.loess	0.251	0.018	0.268
rra.gene_summary	0.029	0.008	0.036
rra.sgrna_summary	0.226	0.018	0.244
sgRankView	0.954	0.405	0.617