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) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:19 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (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 | ||||
|
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. |
| Package 1728/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scMAGeCK 1.6.0 (landing page) Xiaolong Cheng
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| 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 |
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### Running command:
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### 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
###
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* 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.
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
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
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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
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scMAGeCK.Rcheck/examples_i386/scMAGeCK-Ex.timings
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scMAGeCK.Rcheck/examples_x64/scMAGeCK-Ex.timings
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