Habil Zare
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/Pigengene |
| git_branch: master |
| git_last_commit: 8fd8fbe |
| git_last_commit_date: 2022-02-09 17:31:05 -0400 (Wed, 09 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:18 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 Pigengene package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Pigengene.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1428/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Pigengene 1.21.38 (landing page) Habil Zare
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: Pigengene |
| Version: 1.21.38 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Pigengene.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Pigengene_1.21.38.tar.gz |
| StartedAt: 2022-03-17 19:52:37 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 20:02:02 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 564.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Pigengene.Rcheck |
| Warnings: 0 |
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### Running command:
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### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Pigengene.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings Pigengene_1.21.38.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/Pigengene.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Pigengene/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Pigengene' version '1.21.38'
* 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 'Pigengene' 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
* 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
'library' or 'require' calls in package code:
'AnnotationDbi' 'biomaRt' 'energy' 'org.Hs.eg.db' 'org.Mm.eg.db'
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
Found the following possibly unsafe calls:
File 'Pigengene/R/bn.calculation.R':
assignInNamespace("supported.clusters", fixArgs, "bnlearn")
one.step.pigengene: no visible binding for global variable
'org.Hs.eg.db'
Undefined global functions or variables:
org.Hs.eg.db
* 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 data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Pigengene-package 65.33 4.38 70.72
one.step.pigengene 57.84 3.47 62.38
get.enriched.pw 52.44 5.72 58.19
module.heatmap 32.17 5.59 38.15
learn.bn 15.00 0.28 16.18
gene.mapping 13.53 0.61 18.71
make.filter 13.62 0.25 13.88
compact.tree 12.41 0.88 13.30
make.decision.tree 12.52 0.06 12.57
combine.networks 11.94 0.06 12.06
apply.filter 11.32 0.32 11.64
determine.modules 10.94 0.05 11.02
wgcna.one.step 9.30 0.03 9.33
compute.pigengene 5.31 0.97 6.30
plot.pigengene 4.88 1.03 5.92
pigengene 5.01 0.69 5.70
* 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: 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/Pigengene.Rcheck/00check.log'
for details.
Pigengene.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL Pigengene
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'Pigengene' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'Pigengene'
finding HTML links ... done
Pigengene-package html
aml html
apply.filter html
balance html
calculate.beta html
check.nas html
check.pigengene.input html
combine.networks html
compact.tree html
compute.pigengene html
dcor.matrix html
determine.modules html
draw.bn html
eigengenes33 html
gene.mapping html
get.enriched.pw html
get.fitted.leaf html
get.genes html
get.used.features html
learn.bn html
make.decision.tree html
make.filter html
mds html
message.if html
module.heatmap html
one.step.pigengene html
pheatmap.type html
pigengene-class html
pigengene html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-Pigengene/00new/Pigengene/help/pigengene.html
plot.pigengene html
preds.at html
project.eigen html
pvalues.manova html
save.if html
wgcna.one.step 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
* DONE (Pigengene)
Making 'packages.html' ... done
Pigengene.Rcheck/Pigengene-Ex.timings
| name | user | system | elapsed | |
| Pigengene-package | 65.33 | 4.38 | 70.72 | |
| aml | 0.11 | 0.05 | 0.15 | |
| apply.filter | 11.32 | 0.32 | 11.64 | |
| balance | 0.32 | 0.15 | 0.47 | |
| calculate.beta | 0.66 | 0.04 | 0.70 | |
| check.nas | 0.03 | 0.00 | 0.05 | |
| check.pigengene.input | 0.03 | 0.00 | 0.03 | |
| combine.networks | 11.94 | 0.06 | 12.06 | |
| compact.tree | 12.41 | 0.88 | 13.30 | |
| compute.pigengene | 5.31 | 0.97 | 6.30 | |
| dcor.matrix | 0.14 | 0.09 | 0.23 | |
| determine.modules | 10.94 | 0.05 | 11.02 | |
| draw.bn | 0 | 0 | 0 | |
| eigengenes33 | 0.09 | 0.00 | 0.10 | |
| gene.mapping | 13.53 | 0.61 | 18.71 | |
| get.enriched.pw | 52.44 | 5.72 | 58.19 | |
| get.fitted.leaf | 0.39 | 0.07 | 0.46 | |
| get.genes | 0.34 | 0.07 | 0.43 | |
| get.used.features | 0.47 | 0.07 | 0.53 | |
| learn.bn | 15.00 | 0.28 | 16.18 | |
| make.decision.tree | 12.52 | 0.06 | 12.57 | |
| make.filter | 13.62 | 0.25 | 13.88 | |
| mds | 0.10 | 0.02 | 0.11 | |
| message.if | 0 | 0 | 0 | |
| module.heatmap | 32.17 | 5.59 | 38.15 | |
| one.step.pigengene | 57.84 | 3.47 | 62.38 | |
| pheatmap.type | 0.21 | 0.01 | 0.22 | |
| pigengene | 5.01 | 0.69 | 5.70 | |
| plot.pigengene | 4.88 | 1.03 | 5.92 | |
| preds.at | 0.50 | 0.02 | 0.52 | |
| project.eigen | 4.20 | 0.61 | 4.83 | |
| pvalues.manova | 0.03 | 0.00 | 0.04 | |
| save.if | 0.56 | 0.03 | 0.60 | |
| wgcna.one.step | 9.30 | 0.03 | 9.33 | |