Hao Wu
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/PROPER |
| git_branch: RELEASE_3_14 |
| git_last_commit: bc04d64 |
| git_last_commit_date: 2021-10-26 12:18:05 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:07 -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 PROPER package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PROPER.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 1471/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PROPER 1.26.0 (landing page) Hao Wu
| 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: PROPER |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PROPER.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PROPER_1.26.0.tar.gz |
| StartedAt: 2022-04-13 00:53:40 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 00:55:02 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 82.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: PROPER.Rcheck |
| Warnings: 2 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PROPER.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings PROPER_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/PROPER.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 'PROPER/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PROPER' version '1.26.0'
* 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 'PROPER' 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 ... WARNING
'library' or 'require' call not declared from: 'edgeR'
'library' or 'require' calls in package code:
'DESeq2' 'DSS' 'edgeR'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'edgeR'
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
RNAseq.SimOptions.2grp: no visible global function definition for
'data'
RNAseq.SimOptions.2grp: no visible binding for global variable 'cheung'
add.axis1: no visible global function definition for 'axis'
add.axis1: no visible global function definition for 'text'
comparePower: no visible global function definition for 'p.adjust'
estParam: no visible global function definition for 'exprs'
getDisp1: no visible global function definition for 'median'
getDisp2: no visible global function definition for 'DGEList'
getDisp2: no visible global function definition for
'estimateCommonDisp'
getDisp2: no visible global function definition for
'estimateTrendedDisp'
getDisp2: no visible global function definition for
'estimateTagwiseDisp'
lfc.alt: no visible global function definition for 'rnorm'
lfc.null: no visible global function definition for 'rnorm'
plotAll: no visible global function definition for 'par'
plotAll: no visible global function definition for 'mtext'
plotFDR: no visible global function definition for 'matplot'
plotFDR: no visible global function definition for 'mtext'
plotFDR: no visible global function definition for 'axis'
plotFDR: no visible global function definition for 'box'
plotFDR: no visible global function definition for 'grid'
plotFDR: no visible global function definition for 'legend'
plotFDcost : <anonymous>: no visible global function definition for
'sd'
plotFDcost: no visible global function definition for 'matplot'
plotFDcost: no visible global function definition for 'arrows'
plotFDcost: no visible global function definition for 'mtext'
plotFDcost: no visible global function definition for 'axis'
plotFDcost: no visible global function definition for 'box'
plotFDcost: no visible global function definition for 'grid'
plotFDcost: no visible global function definition for 'legend'
plotPower: no visible binding for global variable 'sd'
plotPower: no visible global function definition for 'matplot'
plotPower: no visible global function definition for 'arrows'
plotPower: no visible global function definition for 'mtext'
plotPower: no visible global function definition for 'legend'
plotPower: no visible global function definition for 'grid'
plotPower: no visible global function definition for 'axis'
plotPower: no visible global function definition for 'box'
plotPowerAlpha: no visible binding for global variable 'sd'
plotPowerAlpha: no visible global function definition for 'matplot'
plotPowerAlpha: no visible global function definition for 'arrows'
plotPowerAlpha: no visible global function definition for 'mtext'
plotPowerAlpha: no visible global function definition for 'axis'
plotPowerAlpha: no visible global function definition for 'box'
plotPowerAlpha: no visible global function definition for 'grid'
plotPowerAlpha: no visible global function definition for 'abline'
plotPowerAlpha: no visible global function definition for 'legend'
plotPowerFD: no visible binding for global variable 'sd'
plotPowerFD: no visible global function definition for 'matplot'
plotPowerFD: no visible global function definition for 'arrows'
plotPowerFD: no visible global function definition for 'mtext'
plotPowerFD: no visible global function definition for 'axis'
plotPowerFD: no visible global function definition for 'box'
plotPowerFD: no visible global function definition for 'grid'
plotPowerFD: no visible global function definition for 'legend'
plotPowerHist: no visible global function definition for 'axis'
plotPowerTD: no visible binding for global variable 'sd'
plotPowerTD: no visible global function definition for 'matplot'
plotPowerTD: no visible global function definition for 'arrows'
plotPowerTD: no visible global function definition for 'mtext'
plotPowerTD: no visible global function definition for 'axis'
plotPowerTD: no visible global function definition for 'box'
plotPowerTD: no visible global function definition for 'grid'
plotPowerTD: no visible global function definition for 'legend'
rnegbinom: no visible global function definition for 'rpois'
rnegbinom: no visible global function definition for 'rgamma'
run.DESeq2: no visible global function definition for
'DESeqDataSetFromMatrix'
run.DESeq2: no visible global function definition for 'DataFrame'
run.DESeq2: no visible global function definition for 'DESeq'
run.DESeq2: no visible global function definition for 'results'
run.DSS: no visible global function definition for 'newSeqCountSet'
run.DSS: no visible global function definition for 'estNormFactors'
run.DSS: no visible global function definition for 'estDispersion'
run.DSS: no visible global function definition for 'waldTest'
run.edgeR: no visible global function definition for 'DGEList'
run.edgeR: no visible global function definition for 'calcNormFactors'
run.edgeR: no visible global function definition for
'estimateCommonDisp'
run.edgeR: no visible global function definition for
'estimateTagwiseDisp'
run.edgeR: no visible global function definition for 'exactTest'
run.edgeR: no visible global function definition for 'topTags'
runSims: no visible global function definition for 'median'
setBaselineExpr.seqDepth: no visible global function definition for
'data'
table2hist: no visible global function definition for 'hist'
table2hist: no visible global function definition for 'rnorm'
table2hist: no visible global function definition for 'axis'
table2hist: no visible global function definition for 'box'
Undefined global functions or variables:
DESeq DESeqDataSetFromMatrix DGEList DataFrame abline arrows axis box
calcNormFactors cheung data estDispersion estNormFactors
estimateCommonDisp estimateTagwiseDisp estimateTrendedDisp exactTest
exprs grid hist legend matplot median mtext newSeqCountSet p.adjust
par results rgamma rnorm rpois sd text topTags waldTest
Consider adding
importFrom("graphics", "abline", "arrows", "axis", "box", "grid",
"hist", "legend", "matplot", "mtext", "par", "text")
importFrom("stats", "median", "p.adjust", "rgamma", "rnorm", "rpois",
"sd")
importFrom("utils", "data")
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 ... WARNING
Codoc mismatches from documentation object 'estParam':
estParam
Code: function(X, type = 1)
Docs: function(X, type = c(1, 2))
Mismatches in argument default values:
Name: 'type' Code: 1 Docs: c(1, 2)
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runSims 27.02 0.23 27.27
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
runSims 19.19 0.2 19.41
* 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 WARNINGs, 1 NOTE
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/PROPER.Rcheck/00check.log'
for details.
PROPER.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/PROPER_1.26.0.tar.gz && rm -rf PROPER.buildbin-libdir && mkdir PROPER.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PROPER.buildbin-libdir PROPER_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL PROPER_1.26.0.zip && rm PROPER_1.26.0.tar.gz PROPER_1.26.0.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
88 1596k 88 1415k 0 0 1513k 0 0:00:01 --:--:-- 0:00:01 1512k
100 1596k 100 1596k 0 0 1578k 0 0:00:01 0:00:01 --:--:-- 1580k
install for i386
* installing *source* package 'PROPER' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'PROPER'
finding HTML links ... done
RNAseq.SimOptions.2grp html
comparePower html
estParam html
historicalData html
plotPowerHist html
plots html
power.seqDepth html
runSims html
simRNAseq html
summaryPower 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 'PROPER' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PROPER' as PROPER_1.26.0.zip
* DONE (PROPER)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'PROPER' successfully unpacked and MD5 sums checked
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PROPER.Rcheck/examples_i386/PROPER-Ex.timings
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PROPER.Rcheck/examples_x64/PROPER-Ex.timings
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