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This page was generated on 2022-04-13 12:07:19 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

CHECK results for scMAGeCK on tokay2


To the developers/maintainers of the scMAGeCK package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scMAGeCK.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1728/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scMAGeCK 1.6.0  (landing page)
Xiaolong Cheng
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/scMAGeCK
git_branch: RELEASE_3_14
git_last_commit: 194b6e1
git_last_commit_date: 2021-10-26 12:56:44 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: scMAGeCK
Version: 1.6.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scMAGeCK.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scMAGeCK_1.6.0.tar.gz
StartedAt: 2022-04-13 02:26:53 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 02:37:40 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 646.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: scMAGeCK.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:scMAGeCK.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings scMAGeCK_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/scMAGeCK.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'scMAGeCK/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'scMAGeCK' version '1.6.0'
* 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 ... OK
* checking whether package 'scMAGeCK' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
License components which are templates and need '+ file LICENSE':
  BSD_2_clause
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... WARNING
'::' or ':::' import not declared from: 'purrr'
'library' or 'require' call to 'utils' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot_gi_genes: warning in position_jitter(w = 0.1, h = 0): partial
  argument match of 'w' to 'width'
plot_gi_genes: warning in position_jitter(w = 0.1, h = 0): partial
  argument match of 'h' to 'height'
plot_single_genes: warning in position_jitter(w = 0.1, h = 0): partial
  argument match of 'w' to 'width'
plot_single_genes: warning in position_jitter(w = 0.1, h = 0): partial
  argument match of 'h' to 'height'
KO_eff: no visible global function definition for 'capFirst'
KO_eff: no visible global function definition for 'adjust'
KO_eff: no visible binding for global variable 'padj'
KO_eff: no visible binding for global variable 'lrsc'
KO_eff: no visible binding for global variable 'logpadj'
dis_grna: no visible global function definition for 'read.delim'
dis_grna: no visible binding for global variable 'cell'
dis_grna: no visible binding for global variable 'number_gRNA'
dis_grna: no visible binding for global variable 'ncell'
featurePlot: no visible binding for global variable 'plot.type'
featurePlot: no visible binding for global variable 'cell'
featurePlot: no visible binding for global variable 'number_gRNA'
featurePlot: no visible binding for global variable 'ncell'
featurePlot: no visible binding for global variable 'seurat_clusters'
featurePlot: no visible global function definition for 'wilcox.test'
featurePlot: no visible binding for global variable 'label'
featurePlot: no visible binding for global variable 'genes'
featurePlot: no visible global function definition for
  'colorRampPalette'
featurePlot: no visible binding for global variable 'UMAP_1'
featurePlot: no visible binding for global variable 'UMAP_2'
featurePlot: no visible binding for global variable 'level'
get_rank_tables: no visible global function definition for
  'getoriginalgseascore'
get_sc_signature: no visible binding for global variable 'gs_c2_exps'
getsigmat: no visible global function definition for 'capitalize'
plot_gi_genes: no visible binding for global variable 'Type'
plot_gi_genes: no visible binding for global variable 'Expression'
plot_single_genes: no visible binding for global variable 'targetobj'
plot_single_genes: no visible binding for global variable 'Type'
plot_single_genes: no visible binding for global variable 'Expression'
pre_processRDS: no visible binding for global variable 'cell'
scmageck_rra: no visible global function definition for 'read.delim'
scmageck_rra: no visible global function definition for 'capitalize'
sel_lr: no visible global function definition for 'setNames'
sel_lr: no visible binding for global variable 'sgRNA'
sel_lr: no visible binding for global variable 'FDR'
sel_lr: no visible binding for global variable 'padj'
sel_lr: no visible binding for global variable 'genes'
sel_rra: no visible global function definition for 'read.delim'
sel_rra: no visible binding for global variable 'p.high'
sel_rra: no visible binding for global variable 'p.low'
sel_rra: no visible binding for global variable 'nscore'
sel_rra: no visible binding for global variable 'pscore'
sel_rra: no visible binding for global variable 'index'
sel_rra: no visible binding for global variable 'markers'
sel_rra: no visible binding for global variable 'FDR'
selectPlot: no visible binding for global variable 'select.type'
selectPlot: no visible global function definition for 'setNames'
selectPlot: no visible binding for global variable 'sgRNA'
selectPlot: no visible binding for global variable 'FDR'
selectPlot: no visible binding for global variable 'padj'
selectPlot: no visible binding for global variable 'genes'
selectPlot: no visible binding for global variable 'p.high'
selectPlot: no visible binding for global variable 'p.low'
selectPlot: no visible binding for global variable 'sel_score1'
selectPlot: no visible binding for global variable 'sel_score2'
selectPlot: no visible binding for global variable 'index'
selectPlot: no visible binding for global variable 'markers'
violin_plot: no visible global function definition for 'read.delim'
violin_plot: no visible binding for global variable 'seurat_clusters'
violin_plot: no visible global function definition for 'wilcox.test'
violin_plot: no visible binding for global variable 'label'
violin_plot: no visible binding for global variable 'genes'
Undefined global functions or variables:
  Expression FDR Type UMAP_1 UMAP_2 adjust capFirst capitalize cell
  colorRampPalette genes getoriginalgseascore gs_c2_exps index label
  level logpadj lrsc markers ncell nscore number_gRNA p.high p.low padj
  plot.type pscore read.delim sel_score1 sel_score2 select.type
  setNames seurat_clusters sgRNA targetobj wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "setNames", "wilcox.test")
  importFrom("utils", "read.delim")
to your NAMESPACE file.
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
featurePlot      118.32   0.97  119.58
pre_processRDS    76.00   1.33   77.33
selectPlot        16.84   1.40   18.25
scmageck_lr       16.35   1.40   17.74
scmageck-package  16.53   0.46   17.00
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
featurePlot      115.99   0.30  116.30
pre_processRDS    82.06   0.23   82.29
scmageck-package  21.66   1.35   23.00
scmageck_lr       19.69   2.06   21.75
selectPlot        18.33   2.00   20.33
* 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
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/scMAGeCK.Rcheck/00check.log'
for details.



Installation output

scMAGeCK.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/scMAGeCK_1.6.0.tar.gz && rm -rf scMAGeCK.buildbin-libdir && mkdir scMAGeCK.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scMAGeCK.buildbin-libdir scMAGeCK_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL scMAGeCK_1.6.0.zip && rm scMAGeCK_1.6.0.tar.gz scMAGeCK_1.6.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3050k  100 3050k    0     0  3239k      0 --:--:-- --:--:-- --:--:-- 3241k

install for i386

* installing *source* package 'scMAGeCK' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scMAGeCK'
    finding HTML links ... done
    featurePlot                             html  
    pre_processRDS                          html  
    scmageck-package                        html  
    scmageck_lr                             html  
    scmageck_rra                            html  
    selectPlot                              html  
** 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

install for x64

* installing *source* package 'scMAGeCK' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scMAGeCK' as scMAGeCK_1.6.0.zip
* DONE (scMAGeCK)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'scMAGeCK' successfully unpacked and MD5 sums checked

Tests output


Example timings

scMAGeCK.Rcheck/examples_i386/scMAGeCK-Ex.timings

nameusersystemelapsed
featurePlot118.32 0.97119.58
pre_processRDS76.00 1.3377.33
scmageck-package16.53 0.4617.00
scmageck_lr16.35 1.4017.74
scmageck_rra000
selectPlot16.84 1.4018.25

scMAGeCK.Rcheck/examples_x64/scMAGeCK-Ex.timings

nameusersystemelapsed
featurePlot115.99 0.30116.30
pre_processRDS82.06 0.2382.29
scmageck-package21.66 1.3523.00
scmageck_lr19.69 2.0621.75
scmageck_rra0.010.000.01
selectPlot18.33 2.0020.33