Wentao Yang
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/ABSSeq |
| git_branch: RELEASE_3_14 |
| git_last_commit: b237c96 |
| git_last_commit_date: 2021-10-26 12:12:45 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:08 -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 ABSSeq package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ABSSeq.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 10/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ABSSeq 1.48.0 (landing page) Wentao Yang
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ABSSeq |
| Version: 1.48.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ABSSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ABSSeq_1.48.0.tar.gz |
| StartedAt: 2022-04-12 15:22:53 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 15:27:10 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 257.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ABSSeq.Rcheck |
| Warnings: 0 |
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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:ABSSeq.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings ABSSeq_1.48.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/ABSSeq.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 'ABSSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ABSSeq' version '1.48.0'
* 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 'ABSSeq' 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
'library' or 'require' call to 'edgeR' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ABSDataSet: no visible global function definition for 'new'
ABSSeqlm: no visible global function definition for 'pnorm'
ABSSeqlm: no visible global function definition for 'p.adjust'
ReplaceOutliersByMAD: no visible global function definition for 'is'
ReplaceOutliersByMAD: no visible global function definition for
'model.matrix'
ReplaceOutliersByMAD: no visible global function definition for
'predict'
aFoldcomplexDesign: no visible binding for global variable 'sd'
aFoldcomplexDesign: no visible binding for global variable 'var'
aFoldcomplexDesign: no visible global function definition for 'sd'
callDEs: no visible global function definition for 'is'
callDEs: no visible binding for global variable 'p.adjust.methods'
callDEs: no visible global function definition for 'pnorm'
callDEs: no visible global function definition for 'pnbinom'
callDEs: no visible global function definition for 'p.adjust'
callParameter: no visible global function definition for 'is'
callParameter: no visible binding for global variable 'var'
callParameter: no visible global function definition for 'quantile'
callParameter: no visible global function definition for 'predict'
callParameter: no visible global function definition for 'model.matrix'
callParameterwithoutReplicates: no visible global function definition
for 'is'
callParameterwithoutReplicates: no visible binding for global variable
'sd'
callParameterwithoutReplicates: no visible global function definition
for 'predict'
callParameterwithoutReplicates: no visible binding for global variable
'var'
callParameterwithoutReplicates: no visible global function definition
for 'quantile'
callParameterwithoutReplicates: no visible global function definition
for 'model.matrix'
callPergroup: no visible binding for global variable 'var'
estimateSizeFactorsForMatrix: no visible binding for global variable
'median'
genAFold: no visible binding for global variable 'var'
genAFold: no visible binding for global variable 'sd'
genAFold: no visible global function definition for 'sd'
normalFactors: no visible global function definition for 'is'
normalFactors: no visible global function definition for 'validObject'
normalFactors : rowQuar: no visible global function definition for
'quantile'
normalFactors: no visible global function definition for
'calcNormFactors'
plotDifftoBase: no visible global function definition for 'is'
preAFold: no visible global function definition for 'quantile'
preAFold: no visible global function definition for 'var'
preAFold: no visible global function definition for 'predict'
preAFoldComplex: no visible global function definition for 'quantile'
preAFoldComplex: no visible global function definition for 'var'
preAFoldComplex: no visible global function definition for 'predict'
qtotalNormalized : rowQuar: no visible global function definition for
'quantile'
qtotalNormalized : rowQuar: no visible global function definition for
'sd'
qtotalNormalized : rowQuar: no visible global function definition for
'median'
qtotalNormalized : rowQuar : <anonymous>: no visible global function
definition for 'median'
replaceByrow: no visible global function definition for 'median'
replaceByrow: no visible global function definition for 'mad'
LevelstoNormFC<-,ABSDataSet-numeric: no visible global function
definition for 'validObject'
[[<-,SumInfo-character-missing: no visible global function definition
for 'as'
counts<-,ABSDataSet-matrix: no visible global function definition for
'validObject'
excounts<-,ABSDataSet-matrix: no visible global function definition for
'validObject'
groups<-,ABSDataSet-factor: no visible global function definition for
'validObject'
maxRates<-,ABSDataSet-numeric: no visible global function definition
for 'validObject'
minRates<-,ABSDataSet-numeric: no visible global function definition
for 'validObject'
minimalDispersion<-,ABSDataSet-numeric: no visible global function
definition for 'validObject'
normMethod<-,ABSDataSet-character: no visible global function
definition for 'validObject'
paired<-,ABSDataSet-logical: no visible global function definition for
'validObject'
sFactors<-,ABSDataSet-numeric: no visible global function definition
for 'validObject'
Undefined global functions or variables:
as calcNormFactors is mad median model.matrix new p.adjust
p.adjust.methods pnbinom pnorm predict quantile sd validObject var
Consider adding
importFrom("methods", "as", "is", "new", "validObject")
importFrom("stats", "mad", "median", "model.matrix", "p.adjust",
"p.adjust.methods", "pnbinom", "pnorm", "predict",
"quantile", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotDifftoBase 9.91 0.03 9.93
callParameter 9.77 0.00 9.77
ABSSeq 9.71 0.04 9.76
callDEs 9.68 0.02 9.70
results 9.35 0.01 9.37
excounts 7.95 0.00 7.95
ReplaceOutliersByMAD 7.80 0.01 7.81
ABSSeqlm 6.72 0.04 6.76
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotDifftoBase 10.66 0.00 10.67
callDEs 10.14 0.02 10.15
results 9.75 0.01 9.78
ABSSeq 9.58 0.03 9.61
callParameter 9.58 0.00 9.58
ReplaceOutliersByMAD 7.80 0.02 7.83
excounts 7.44 0.00 7.45
ABSSeqlm 6.15 0.04 6.18
* 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
'C:/Users/biocbuild/bbs-3.14-bioc/meat/ABSSeq.Rcheck/00check.log'
for details.
ABSSeq.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/ABSSeq_1.48.0.tar.gz && rm -rf ABSSeq.buildbin-libdir && mkdir ABSSeq.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ABSSeq.buildbin-libdir ABSSeq_1.48.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL ABSSeq_1.48.0.zip && rm ABSSeq_1.48.0.tar.gz ABSSeq_1.48.0.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
87 225k 87 197k 0 0 658k 0 --:--:-- --:--:-- --:--:-- 658k
100 225k 100 225k 0 0 749k 0 --:--:-- --:--:-- --:--:-- 750k
install for i386
* installing *source* package 'ABSSeq' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ABSSeq'
finding HTML links ... done
ABSDataSet html
ABSSeq html
ABSSeqlm html
LevelstoNormFC html
ReplaceOutliersByMAD html
aFoldcomplexDesign html
callDEs html
callParameter html
callParameterwithoutReplicates html
counts html
estimateSizeFactorsForMatrix html
excounts html
genAFold html
groups html
maxRates html
minRates html
minimalDispersion html
normMethod html
normalFactors html
paired html
plotDifftoBase html
qtotalNormalized html
results html
sFactors html
simuN5 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 'ABSSeq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ABSSeq' as ABSSeq_1.48.0.zip
* DONE (ABSSeq)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'ABSSeq' successfully unpacked and MD5 sums checked
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ABSSeq.Rcheck/examples_i386/ABSSeq-Ex.timings
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ABSSeq.Rcheck/examples_x64/ABSSeq-Ex.timings
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