Zhilong Jia
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/cogena |
| git_branch: RELEASE_3_14 |
| git_last_commit: 639d8fb |
| git_last_commit_date: 2021-10-26 12:19:56 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:22 -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 cogena package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cogena.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 369/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cogena 1.28.0 (landing page) Zhilong Jia
| 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: cogena |
| Version: 1.28.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cogena.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cogena_1.28.0.tar.gz |
| StartedAt: 2022-04-12 17:42:56 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 17:49:59 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 422.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: cogena.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cogena.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cogena_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cogena.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 'cogena/DESCRIPTION' ... OK
* this is package 'cogena' version '1.28.0'
* 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 'cogena' can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
See 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cogena.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 5.1Mb
sub-directories of 1Mb or more:
extdata 3.6Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
dist.fn: no visible global function definition for 'cor'
heatmap.3: no visible binding for global variable 'dist'
heatmap.3: no visible global function definition for 'par'
heatmap.3: no visible global function definition for 'median'
heatmap.3: no visible global function definition for 'order.dendrogram'
heatmap.3: no visible global function definition for 'reorder'
heatmap.3: no visible binding for global variable 'sd'
heatmap.3: no visible global function definition for 'layout'
heatmap.3: no visible global function definition for 'image'
heatmap.3: no visible global function definition for 'axis'
heatmap.3: no visible global function definition for 'mtext'
heatmap.3: no visible global function definition for 'rect'
heatmap.3: no visible global function definition for 'abline'
heatmap.3: no visible global function definition for 'lines'
heatmap.3: no visible global function definition for 'text'
heatmap.3: no visible global function definition for 'plot.new'
heatmap.3: no visible global function definition for 'title'
heatmap.3: no visible global function definition for 'density'
heatmap.3: no visible global function definition for 'hist'
plot.sota: no visible global function definition for 'par'
corInCluster,cogena: no visible global function definition for 'cor'
heatmapCluster,cogena: no visible global function definition for
'topo.colors'
heatmapCluster,cogena: no visible global function definition for
'rainbow'
heatmapCluster,cogena: no visible global function definition for 'par'
heatmapCluster,cogena: no visible global function definition for
'legend'
heatmapPEI,cogena: no visible binding for global variable 'clusterID'
heatmapPEI,cogena: no visible binding for global variable 'TF'
heatmapPEI,cogena: no visible binding for global variable
'clusterNumGene'
heatmapPEI,cogena: no visible binding for global variable 'GS'
heatmapPEI,cogena: no visible binding for global variable 'value'
heatmapPEI,cogena: no visible binding for global variable 'GeneCount'
Undefined global functions or variables:
GS GeneCount TF abline axis clusterID clusterNumGene cor density dist
hist image layout legend lines median mtext order.dendrogram par
plot.new rainbow rect reorder sd text title topo.colors value
Consider adding
importFrom("grDevices", "rainbow", "topo.colors")
importFrom("graphics", "abline", "axis", "hist", "image", "layout",
"legend", "lines", "mtext", "par", "plot.new", "rect",
"text", "title")
importFrom("stats", "cor", "density", "dist", "median",
"order.dendrogram", "reorder", "sd")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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
cogena_package 7.05 0.82 88.84
clEnrich_one 3.88 0.16 13.19
clEnrich 3.17 0.15 18.98
upDownGene 2.43 0.28 17.09
clusterMethods 1.34 0.03 10.67
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
cogena_package 6.70 0.93 82.98
clEnrich_one 3.71 0.16 12.84
upDownGene 2.28 0.22 17.10
clEnrich 2.28 0.18 16.88
clusterMethods 1.18 0.03 9.72
* 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/cogena.Rcheck/00check.log'
for details.
cogena.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/cogena_1.28.0.tar.gz && rm -rf cogena.buildbin-libdir && mkdir cogena.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cogena.buildbin-libdir cogena_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cogena_1.28.0.zip && rm cogena_1.28.0.tar.gz cogena_1.28.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
14 4588k 14 673k 0 0 993k 0 0:00:04 --:--:-- 0:00:04 993k
56 4588k 56 2574k 0 0 1532k 0 0:00:02 0:00:01 0:00:01 1533k
100 4588k 100 4588k 0 0 1897k 0 0:00:02 0:00:02 --:--:-- 1897k
install for i386
* installing *source* package 'cogena' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
** help
*** installing help indices
converting help for package 'cogena'
finding HTML links ... done
AllGeneSymbols html
DEexprs html
PEI html
Psoriasis html
clEnrich html
clEnrich_one html
clusterMethods html
coExp html
cogena_class html
cogena_package html
corInCluster html
enrichment html
gene2set html
geneExpInCluster html
geneInCluster html
genecl_class html
geneclusters html
gmt2list html
gmtlist2file html
heatmap.3 html
heatmapCluster html
heatmapCmap html
heatmapPEI html
mat html
nClusters html
pClusters html
sampleLabel html
show html
sota html
summary html
upDownGene html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'cogena' ...
** testing if installed package can be loaded
Warning: replacing previous import 'class::somgrid' by 'kohonen::somgrid' when loading 'cogena'
* MD5 sums
packaged installation of 'cogena' as cogena_1.28.0.zip
* DONE (cogena)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'cogena' successfully unpacked and MD5 sums checked
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cogena.Rcheck/examples_i386/cogena-Ex.timings
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cogena.Rcheck/examples_x64/cogena-Ex.timings
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