Maia Smith
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/cellscape |
| Branch: RELEASE_3_7 |
| Last Commit: c6fd589 |
| Last Changed Date: 2018-04-30 10:35:45 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:43:32 -0400 (Wed, 17 Oct 2018).
| Package 206/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| cellscape 1.4.0 Maia Smith
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: cellscape |
| Version: 1.4.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellscape.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cellscape_1.4.0.tar.gz |
| StartedAt: 2018-10-17 00:59:06 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 00:59:53 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 47.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cellscape.Rcheck |
| Warnings: 1 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cellscape.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings cellscape_1.4.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/cellscape.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cellscape/DESCRIPTION' ... OK
* this is package 'cellscape' version '1.4.0'
* 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 'cellscape' 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
* 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 ... NOTE
Namespace in Imports field not imported from: 'plyr'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
cellscape: no visible global function definition for 'setNames'
cellscape: no visible global function definition for 'melt'
cellscape: no visible global function definition for 'na.omit'
cellscape: no visible global function definition for 'combn'
cellscape: no visible binding for global variable 'site'
cellscape: no visible binding for global variable 'genotype'
cellscape: no visible binding for global variable 'VAF'
cellscape: no visible global function definition for 'n'
cellscape: no visible binding for global variable 'n_gt'
cellscape: no visible binding for global variable 'n'
cellscape: no visible binding for global variable 'timepoint'
cellscape: no visible binding for global variable 'single_cell_id'
getCNVHeatmapForEachSC: no visible binding for global variable
'single_cell_id'
getCNVHeatmapForEachSC: no visible binding for global variable 'px'
getCNVHeatmapForEachSC: no visible binding for global variable
'px_width'
getCNVHeatmapForEachSC: no visible binding for global variable 'chr'
getCNVHeatmapForEachSC: no visible binding for global variable
'chrom_index'
getCNVHeatmapForEachSC: no visible binding for global variable
'copy_number'
getCNVHeatmapForEachSC: no visible binding for global variable 'sc_id'
getCNVHeatmapForEachSC: no visible binding for global variable
'mode_cnv'
getCNVHeatmapForEachSC: no visible binding for global variable
'cumsum_values'
getMutOrder: no visible global function definition for 'dist'
getMutOrder: no visible global function definition for 'hclust'
getMutOrder: no visible binding for global variable 'site'
getMutOrder: no visible binding for global variable 'VAF'
getMutOrder: no visible global function definition for 'lm'
getMutOrder: no visible binding for global variable 'na.omit'
getMutOrder: no visible global function definition for 'coef'
getMutationsData: no visible binding for global variable
'show_warnings'
getTargetedHeatmapForEachSC: no visible binding for global variable
'single_cell_id'
getTargetedHeatmapForEachSC: no visible binding for global variable
'chr'
getTargetedHeatmapForEachSC: no visible binding for global variable
'coord'
Undefined global functions or variables:
VAF chr chrom_index coef combn coord copy_number cumsum_values dist
genotype hclust lm melt mode_cnv n n_gt na.omit px px_width sc_id
setNames show_warnings single_cell_id site timepoint
Consider adding
importFrom("stats", "coef", "dist", "hclust", "lm", "na.omit",
"setNames")
importFrom("utils", "combn")
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 ... WARNING
Duplicated \argument entries in documentation object 'dfs_tree':
'chrom_bounds' 'ncols' 'chrom_bounds' 'cnv_data' 'chrom_bounds'
'n_bp_per_pixel' 'mut_data' 'width' 'height' 'mutations' 'height'
'width' 'clonal_prev' 'tree_edges' 'alpha' 'clonal_prev' 'tree_edges'
'genotype_position' 'clone_colours' 'perturbations' 'mutations'
'tree_edges' 'clonal_prev' 'clonal_prev' 'tree_edges' 'clone_colours'
'mutations'
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
cellscape 2.34 0.45 7.74
** running examples for arch 'x64' ... OK
* 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-3.7-bioc/meat/cellscape.Rcheck/00check.log'
for details.
cellscape.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/cellscape_1.4.0.tar.gz && rm -rf cellscape.buildbin-libdir && mkdir cellscape.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cellscape.buildbin-libdir cellscape_1.4.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL cellscape_1.4.0.zip && rm cellscape_1.4.0.tar.gz cellscape_1.4.0.zip
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100 702k 100 702k 0 0 11.7M 0 --:--:-- --:--:-- --:--:-- 13.1M
install for i386
* installing *source* package 'cellscape' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cellscape'
finding HTML links ... done
cellscape html
helpers html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'cellscape' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cellscape' as cellscape_1.4.0.zip
* DONE (cellscape)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'cellscape' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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cellscape.Rcheck/examples_i386/cellscape-Ex.timings
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cellscape.Rcheck/examples_x64/cellscape-Ex.timings
|