Pedro Lopez-Romero
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/AgiMicroRna |
| git_branch: master |
| git_last_commit: b4bdea1 |
| git_last_commit_date: 2021-10-26 11:54:33 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:06:54 -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 AgiMicroRna package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/AgiMicroRna.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 36/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| AgiMicroRna 2.45.0 (landing page) Pedro Lopez-Romero
| 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: AgiMicroRna |
| Version: 2.45.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:AgiMicroRna.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings AgiMicroRna_2.45.0.tar.gz |
| StartedAt: 2022-03-17 18:25:36 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:31:09 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 332.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: AgiMicroRna.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:AgiMicroRna.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings AgiMicroRna_2.45.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/AgiMicroRna.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 'AgiMicroRna/DESCRIPTION' ... OK
* this is package 'AgiMicroRna' version '2.45.0'
* 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 'AgiMicroRna' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'Biobase'
A package should be listed in only one of these fields.
* 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 ... NOTE
Warning: no function found corresponding to methods exports from 'AgiMicroRna' for: 'show'
A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.
Probably some imports need to be declared in the NAMESPACE file.
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
'affy' 'affycoretools' 'preprocessCore'
Please remove these calls from your code.
'library' or 'require' calls in package code:
'codelink' 'gdata' 'geneplotter' 'gplots' 'gtools' 'marray'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
'affy' 'affycoretools' 'limma' 'methods' 'preprocessCore'
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 ... NOTE
Foreign function call to a different package:
.Call("rma_c_complete_copy", ..., PACKAGE = "affy")
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... NOTE
DEG.print.info: no visible global function definition for 'is'
DEG.print.info: no visible global function definition for 'exprs'
HeatMapMicroRna: no visible binding for global variable 'var'
HeatMapMicroRna: no visible global function definition for 'rainbow'
HeatMapMicroRna: no visible global function definition for 'maPalette'
HeatMapMicroRna: no visible global function definition for 'heatmap.2'
HeatMapMicroRna: no visible global function definition for 'title'
MA.plot.miRNA: no visible global function definition for 'dev.new'
MA.plot.miRNA: no visible global function definition for 'points'
MA.plot.miRNA: no visible global function definition for 'fitted'
MA.plot.miRNA: no visible global function definition for 'loess'
MA.plot.miRNA: no visible global function definition for 'legend'
MA.plot.miRNA: no visible global function definition for 'title'
PCAplotMicroRna: no visible global function definition for 'is'
PCAplotMicroRna: no visible global function definition for 'exprs'
PCAplotMicroRna: no visible global function definition for 'na.omit'
PCAplotMicroRna: no visible global function definition for 'exprs<-'
PCAplotMicroRna: no visible global function definition for 'plotPCA'
PCAplotMicroRna: no visible global function definition for 'dev.new'
RleMicroRna: no visible binding for global variable 'median'
RleMicroRna: no visible global function definition for 'par'
RleMicroRna: no visible global function definition for 'boxplot'
RleMicroRna: no visible global function definition for 'points'
RleMicroRna: no visible global function definition for 'lines'
RleMicroRna: no visible global function definition for 'title'
RleMicroRna: no visible global function definition for 'abline'
basicLimma: no visible global function definition for 'is'
basicLimma: no visible global function definition for 'exprs'
basicLimma: no visible global function definition for 'lmFit'
basicLimma: no visible global function definition for 'contrasts.fit'
basicLimma: no visible global function definition for 'eBayes'
boxplotMicroRna: no visible global function definition for 'par'
boxplotMicroRna: no visible global function definition for 'boxplot'
boxplotMicroRna: no visible global function definition for 'points'
boxplotMicroRna: no visible global function definition for 'lines'
boxplotMicroRna: no visible global function definition for 'title'
cv.array: no visible binding for global variable 'median'
cvArray: no visible global function definition for 'is'
esetMicroRna: no visible global function definition for 'is'
esetMicroRna: no visible global function definition for 'new'
esetMicroRna: no visible global function definition for 'dev.new'
esetMicroRna: no visible global function definition for 'exprs'
filter.IsGeneDetected: no visible global function definition for 'is'
filter.control.miRNA: no visible global function definition for 'is'
filter.wellaboveNEG.miRNA: no visible global function definition for
'is'
filter.wellaboveNEG.miRNA: no visible binding for global variable 'sd'
filterMicroRna: no visible global function definition for 'is'
filterMicroRna: no visible global function definition for 'dev.new'
getDecideTests: no visible global function definition for 'is'
getDecideTests: no visible global function definition for 'decideTests'
hierclusMicroRna: no visible binding for global variable 'var'
hierclusMicroRna: no visible global function definition for 'dist'
hierclusMicroRna: no visible global function definition for 'as.dist'
hierclusMicroRna: no visible global function definition for 'cor'
hierclusMicroRna: no visible global function definition for 'hclust'
hierclusMicroRna: no visible global function definition for 'title'
mvaBASIC: no visible binding for global variable 'median'
mvaBASIC: no visible global function definition for 'title'
mvaBASIC: no visible global function definition for 'abline'
mvaMicroRna: no visible binding for global variable 'median'
mvaMicroRna: no visible global function definition for 'points'
mvaMicroRna: no visible global function definition for 'fitted'
mvaMicroRna: no visible global function definition for 'loess'
mvaMicroRna: no visible global function definition for 'title'
mvaMicroRna: no visible global function definition for 'abline'
mvaMicroRna: no visible global function definition for 'legend'
plotDensityMicroRna: no visible global function definition for
'rainbow'
plotDensityMicroRna: no visible global function definition for
'density'
plotDensityMicroRna: no visible global function definition for 'lines'
plotDensityMicroRna: no visible global function definition for 'title'
plotDensityMicroRna: no visible global function definition for 'legend'
pvalHistogram: no visible global function definition for 'p.adjust'
pvalHistogram: no visible global function definition for 'hist'
pvalHistogram: no visible global function definition for 'dev.new'
qcPlots: no visible global function definition for 'is'
qcPlots: no visible global function definition for 'dev.new'
read.agiMicroRna: no visible global function definition for
'read.columns'
read.agiMicroRna: no visible global function definition for 'new'
readMicroRnaAFE: no visible global function definition for 'is'
readTargets: no visible global function definition for 'read.table'
rmaMicroRna: no visible global function definition for 'is'
rmaMicroRna: no visible global function definition for
'rma.background.correct'
rmaMicroRna: no visible global function definition for
'normalizeBetweenArrays'
rmaMicroRna: no visible binding for global variable 'median'
significantMicroRna: no visible global function definition for 'is'
significantMicroRna: no visible global function definition for 'exprs'
significantMicroRna: no visible global function definition for
'p.adjust'
tgsMicroRna: no visible global function definition for 'is'
tgsMicroRna: no visible global function definition for 'dev.new'
tgsNormalization: no visible global function definition for 'is'
tgsNormalization: no visible global function definition for 'dev.new'
tgsNormalization: no visible global function definition for
'normalizeBetweenArrays'
write.LIST.miRNA: no visible global function definition for 'is'
write.LIST.miRNA: no visible global function definition for
'write.table'
write.control.out.miRNA: no visible global function definition for 'is'
write.control.out.miRNA: no visible global function definition for
'write.table'
write.filt.out.miRNA: no visible global function definition for 'is'
write.filt.out.miRNA: no visible global function definition for
'write.table'
writeEset: no visible global function definition for 'is'
writeEset: no visible global function definition for 'exprs'
writeEset: no visible global function definition for 'featureNames'
writeEset: no visible global function definition for 'write.table'
show,uRNAList: no visible global function definition for 'slotNames'
show,uRNAList: no visible global function definition for 'slot'
Undefined global functions or variables:
abline as.dist boxplot contrasts.fit cor decideTests density dev.new
dist eBayes exprs exprs<- featureNames fitted hclust heatmap.2 hist
is legend lines lmFit loess maPalette median na.omit new
normalizeBetweenArrays p.adjust par plotPCA points rainbow
read.columns read.table rma.background.correct sd slot slotNames
title var write.table
Consider adding
importFrom("grDevices", "dev.new", "rainbow")
importFrom("graphics", "abline", "boxplot", "hist", "legend", "lines",
"par", "points", "title")
importFrom("methods", "is", "new", "slot", "slotNames")
importFrom("stats", "as.dist", "cor", "density", "dist", "fitted",
"hclust", "loess", "median", "na.omit", "p.adjust", "sd",
"var")
importFrom("utils", "read.table", "write.table")
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
mvaMicroRna 16.97 0.38 17.36
* 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: 5 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/AgiMicroRna.Rcheck/00check.log'
for details.
AgiMicroRna.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL AgiMicroRna
###
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* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'AgiMicroRna' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'AgiMicroRna'
finding HTML links ... done
HeatMapMicroRna html
PCAplotMicroRna html
RleMicroRna html
basicLimma html
boxplotMicroRna html
cvArray html
dd.micro html
ddPROC html
dim.uRNAList html
dimnames.uRNAList html
esetMicroRna html
filterMicroRna html
getDecideTests html
hierclusMicroRna html
mvaBASIC html
mvaMicroRna html
plotDensityMicroRna html
pvalHistogram html
qcPlots html
readMicroRnaAFE html
readTargets html
rmaMicroRna html
significantMicroRna html
summary.uRNAList html
targets.micro html
tgsMicroRna html
tgsNormalization html
uRNAList html
writeEset 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 (AgiMicroRna)
Making 'packages.html' ... done
AgiMicroRna.Rcheck/AgiMicroRna-Ex.timings
| name | user | system | elapsed | |
| HeatMapMicroRna | 0.34 | 0.10 | 0.89 | |
| PCAplotMicroRna | 0.2 | 0.0 | 0.2 | |
| RleMicroRna | 0.78 | 0.11 | 0.89 | |
| basicLimma | 0 | 0 | 0 | |
| boxplotMicroRna | 0.39 | 0.00 | 0.39 | |
| cvArray | 0 | 0 | 0 | |
| filterMicroRna | 0.36 | 0.08 | 0.44 | |
| getDecideTests | 0 | 0 | 0 | |
| hierclusMicroRna | 0.05 | 0.00 | 0.05 | |
| mvaBASIC | 2.86 | 0.15 | 3.04 | |
| mvaMicroRna | 16.97 | 0.38 | 17.36 | |
| plotDensityMicroRna | 2.03 | 0.03 | 2.06 | |
| pvalHistogram | 0 | 0 | 0 | |
| qcPlots | 0 | 0 | 0 | |
| readMicroRnaAFE | 0 | 0 | 0 | |
| rmaMicroRna | 4.58 | 0.03 | 4.61 | |
| significantMicroRna | 0.66 | 0.05 | 0.70 | |
| tgsMicroRna | 0.13 | 0.01 | 0.14 | |
| tgsNormalization | 0 | 0 | 0 | |
| uRNAList | 0 | 0 | 0 | |
| writeEset | 0 | 0 | 0 | |