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This page was generated on 2024-06-21 17:39 -0400 (Fri, 21 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4758
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4492
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4506
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4464
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1147/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAGeCKFlute 2.8.0  (landing page)
Wubing Zhang
Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024)
git_url: https://git.bioconductor.org/packages/MAGeCKFlute
git_branch: RELEASE_3_19
git_last_commit: cf8b1d4
git_last_commit_date: 2024-04-30 11:02:57 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for MAGeCKFlute on palomino3

To the developers/maintainers of the MAGeCKFlute package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MAGeCKFlute.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MAGeCKFlute
Version: 2.8.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAGeCKFlute.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MAGeCKFlute_2.8.0.tar.gz
StartedAt: 2024-06-20 06:19:07 -0400 (Thu, 20 Jun 2024)
EndedAt: 2024-06-20 06:26:55 -0400 (Thu, 20 Jun 2024)
EllapsedTime: 468.0 seconds
RetCode: 0
Status:   OK  
CheckDir: MAGeCKFlute.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAGeCKFlute.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings MAGeCKFlute_2.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/MAGeCKFlute.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MAGeCKFlute/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MAGeCKFlute' version '2.8.0'
* 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 whether package 'MAGeCKFlute' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.7Mb
  sub-directories of 1Mb or more:
    extdata  20.3Mb
* 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 code 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
EnrichedFilter: no visible global function definition for 'is'
EnrichedGeneView: no visible global function definition for 'is'
EnrichedView: no visible global function definition for 'is'
EnrichedView: no visible global function definition for 'slot'
enrich.HGT: no visible global function definition for 'new'
Undefined global functions or variables:
  is new slot
Consider adding
  importFrom("methods", "is", "new", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) FluteMLE.Rd:87: Lost braces; missing escapes or markup?
    87 |   \item {QC}: {Quality control}
       |               ^
checkRd: (-1) FluteMLE.Rd:88: Lost braces; missing escapes or markup?
    88 |   \item {Selection}: {Positive selection and negative selection.}
       |                      ^
checkRd: (-1) FluteMLE.Rd:89: Lost braces; missing escapes or markup?
    89 |   \item {Enrichment}: {Enrichment analysis for positive and negative selection genes.}
       |                       ^
checkRd: (-1) FluteMLE.Rd:90: Lost braces; missing escapes or markup?
    90 |   \item {PathwayView}: {Pathway view for top enriched pathways.}
       |                        ^
checkRd: (-1) getOrg.Rd:18: Lost braces
    18 | \code{pkg}{annotation package name}
       |           ^
* 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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
MAView 20.5   0.19   20.69
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/MAGeCKFlute.Rcheck/00check.log'
for details.


Installation output

MAGeCKFlute.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL MAGeCKFlute
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'MAGeCKFlute' ...
** using staged installation
** R
** 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 (MAGeCKFlute)

Tests output


Example timings

MAGeCKFlute.Rcheck/MAGeCKFlute-Ex.timings

nameusersystemelapsed
BarView0.210.030.25
BatchRemove2.161.864.11
ConsistencyView1.250.114.55
CutoffCalling000
DensityDiffView1.090.041.14
DensityView0.860.050.91
EnrichAnalyzer0.020.000.06
EnrichedFilter0.010.000.01
EnrichedGeneView0.020.000.02
EnrichedView0.010.000.02
FluteMLE000
FluteRRA000
HeatmapView0.410.030.45
IdentBarView0.130.020.14
IncorporateDepmap0.370.012.21
MAView20.50 0.1920.69
MapRatesView0.390.000.45
NormalizeBeta0.840.021.25
OmitCommonEssential000
RankView0.940.041.12
ReadBeta0.400.000.41
ReadRRA0.270.020.28
ReadsgRRA0.010.000.19
ResembleDepmap0.220.000.22
ScatterView3.440.063.51
Selector0.590.000.60
SquareView1.210.001.20
TransGeneID1.830.031.89
ViolinView1.620.001.64
VolcanoView2.380.062.44
arrangePathview1.150.021.17
enrich.GSE0.020.000.03
enrich.HGT1.750.061.83
enrich.ORT4.390.174.63
getCols0.000.000.02
getGeneAnn000
getOrg000
getOrtAnn000
gsGetter0.360.000.38
hclustView0.410.040.51
loadDepmap000
normalize.loess1.020.031.05
sgRankView0.180.000.19
writeGMT0.020.000.03