Wentao Yang
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/ABSSeq |
| git_branch: master |
| git_last_commit: e4e5952 |
| git_last_commit_date: 2021-10-26 12:12:45 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:06:53 -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 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? 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 10/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ABSSeq 1.49.0 (landing page) Wentao Yang
| 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 | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ABSSeq |
| Version: 1.49.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ABSSeq.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ABSSeq_1.49.0.tar.gz |
| StartedAt: 2022-03-17 18:25:36 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:27:21 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 105.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ABSSeq.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ABSSeq.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ABSSeq_1.49.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ABSSeq.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 'ABSSeq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ABSSeq' version '1.49.0'
* 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
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
callDEs 7.81 0.31 8.12
results 7.42 0.23 7.66
ABSSeq 6.61 0.99 7.59
callParameter 7.04 0.19 7.22
plotDifftoBase 6.94 0.14 7.08
ReplaceOutliersByMAD 5.40 0.16 5.56
excounts 5.18 0.19 5.36
* 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/ABSSeq.Rcheck/00check.log'
for details.
ABSSeq.Rcheck/00install.out
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ABSSeq
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* 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
* DONE (ABSSeq)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'miRNApath' is missing or broken
done
ABSSeq.Rcheck/ABSSeq-Ex.timings
| name | user | system | elapsed | |
| ABSDataSet | 0.07 | 0.00 | 0.06 | |
| ABSSeq | 6.61 | 0.99 | 7.59 | |
| ABSSeqlm | 4.75 | 0.20 | 4.96 | |
| LevelstoNormFC | 0.03 | 0.00 | 0.03 | |
| ReplaceOutliersByMAD | 5.40 | 0.16 | 5.56 | |
| aFoldcomplexDesign | 2.72 | 0.11 | 2.83 | |
| callDEs | 7.81 | 0.31 | 8.12 | |
| callParameter | 7.04 | 0.19 | 7.22 | |
| callParameterwithoutReplicates | 1.14 | 0.04 | 1.19 | |
| counts | 0.03 | 0.00 | 0.03 | |
| estimateSizeFactorsForMatrix | 0.04 | 0.00 | 0.05 | |
| excounts | 5.18 | 0.19 | 5.36 | |
| genAFold | 2.87 | 0.20 | 3.07 | |
| groups | 0.02 | 0.02 | 0.04 | |
| maxRates | 0.03 | 0.00 | 0.03 | |
| minRates | 0.03 | 0.00 | 0.03 | |
| minimalDispersion | 0.03 | 0.00 | 0.03 | |
| normMethod | 0.03 | 0.00 | 0.03 | |
| normalFactors | 1.88 | 0.06 | 1.94 | |
| paired | 0.03 | 0.00 | 0.03 | |
| plotDifftoBase | 6.94 | 0.14 | 7.08 | |
| qtotalNormalized | 2.14 | 0.10 | 2.23 | |
| results | 7.42 | 0.23 | 7.66 | |
| sFactors | 2.12 | 0.11 | 2.23 | |
| simuN5 | 0.03 | 0.00 | 0.03 | |