| Back to Multiple platform build/check report for BioC 3.14 |
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This page was generated on 2022-04-13 12:06:29 -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 | ||||
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To the developers/maintainers of the DrugVsDisease package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DrugVsDisease.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 545/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DrugVsDisease 2.36.0 (landing page) j. Saez-Rodriguez
| 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: DrugVsDisease |
| Version: 2.36.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DrugVsDisease.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DrugVsDisease_2.36.0.tar.gz |
| StartedAt: 2022-04-12 18:54:37 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 19:00:05 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 327.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: DrugVsDisease.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:DrugVsDisease.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings DrugVsDisease_2.36.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/DrugVsDisease.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 'DrugVsDisease/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DrugVsDisease' version '2.36.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'affy', 'limma', 'biomaRt', 'ArrayExpress', 'GEOquery',
'DrugVsDiseasedata', 'cMap2data', 'qvalue'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'DrugVsDisease' 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' calls to packages already attached by Depends:
'ArrayExpress' 'DrugVsDiseasedata' 'GEOquery' 'affy' 'biomaRt'
'limma' 'qvalue'
Please remove these calls from your code.
Namespaces in Imports field not imported from:
'BiocGenerics' 'RUnit' 'annotate' 'hgu133a.db' 'hgu133a2.db'
'hgu133plus2.db' 'xtable'
All declared Imports should be used.
Packages in Depends field not imported from:
'ArrayExpress' 'DrugVsDiseasedata' 'GEOquery' 'affy' 'biomaRt'
'cMap2data' 'limma' 'qvalue'
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
.averagecluster: no visible binding for global variable 'drugClusters'
.averagecluster: no visible binding for global variable
'diseaseClusters'
.calculateES: no visible binding for global variable 'drugRL'
.calculateES: no visible binding for global variable 'diseaseRL'
.calculateES : <anonymous>: no visible global function definition for
'qvalue'
.convertEnsembl: no visible binding for global variable
'annotationlist'
.convertEnsembl: no visible global function definition for 'useMart'
.convertEnsembl: no visible global function definition for 'getBM'
.datafromAE: no visible global function definition for 'ArrayExpress'
.datafromAE: no visible global function definition for 'annotation'
.datafromAE: no visible global function definition for 'pData'
.datafromGEO: no visible global function definition for 'getGEO'
.datafromGEO: no visible global function definition for 'GDS2eSet'
.datafromGEO: no visible global function definition for 'pData'
.datafromGEO: no visible global function definition for 'annotation'
.datafromGEO: no visible binding for global variable 'GEOfactorvalues'
.datafromGEO: no visible global function definition for 'exprs'
.findCluster: no visible binding for global variable 'drugClusters'
.findCluster: no visible binding for global variable 'diseaseClusters'
.findSignifCompounds: no visible global function definition for
'qvalue'
.fitlms: no visible global function definition for 'lmFit'
.multcontrast: no visible global function definition for
'contrasts.fit'
.multcontrast: no visible global function definition for 'eBayes'
.normalisedata: no visible global function definition for 'rma'
.normalisedata: no visible global function definition for 'mas5'
.readlocalAE: no visible global function definition for 'ReadAffy'
.readlocalCEL: no visible global function definition for 'ReadAffy'
.singlecontrast: no visible global function definition for 'lmFit'
.singlecontrast: no visible global function definition for
'contrasts.fit'
.singlecontrast: no visible global function definition for 'eBayes'
.treatmentonlyfit: no visible global function definition for 'lmFit'
.writecytoscape: no visible binding for global variable 'drugClusters'
.writecytoscape: no visible binding for global variable 'cytodrug'
.writecytoscape: no visible binding for global variable 'druglabels'
.writecytoscape: no visible binding for global variable
'diseaseClusters'
.writecytoscape: no visible binding for global variable 'cytodisease'
.writecytoscape: no visible binding for global variable 'diseaselabels'
generateprofiles: no visible binding for global variable 'genelist'
generateprofiles: no visible global function definition for 'exprs'
Undefined global functions or variables:
ArrayExpress GDS2eSet GEOfactorvalues ReadAffy annotation
annotationlist contrasts.fit cytodisease cytodrug diseaseClusters
diseaseRL diseaselabels drugClusters drugRL druglabels eBayes exprs
genelist getBM getGEO lmFit mas5 pData qvalue rma useMart
* 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 LazyData ... 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
classifyprofile 18.51 4.28 31.59
selectrankedlists 14.77 4.47 19.24
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
classifyprofile 19.66 1.42 21.07
selectrankedlists 13.50 0.84 14.34
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.R'
OK
* 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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/DrugVsDisease.Rcheck/00check.log'
for details.
DrugVsDisease.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/DrugVsDisease_2.36.0.tar.gz && rm -rf DrugVsDisease.buildbin-libdir && mkdir DrugVsDisease.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DrugVsDisease.buildbin-libdir DrugVsDisease_2.36.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL DrugVsDisease_2.36.0.zip && rm DrugVsDisease_2.36.0.tar.gz DrugVsDisease_2.36.0.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
9 1693k 9 165k 0 0 552k 0 0:00:03 --:--:-- 0:00:03 553k
87 1693k 87 1479k 0 0 1137k 0 0:00:01 0:00:01 --:--:-- 1137k
100 1693k 100 1693k 0 0 1199k 0 0:00:01 0:00:01 --:--:-- 1199k
install for i386
* installing *source* package 'DrugVsDisease' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'DrugVsDisease'
finding HTML links ... done
DrugVsDisease-package html
classifyprofile html
combineProfiles html
customClust html
customdb html
customedge html
customsif html
generateprofiles html
profiles html
selectrankedlists html
selprofile 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 'DrugVsDisease' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DrugVsDisease' as DrugVsDisease_2.36.0.zip
* DONE (DrugVsDisease)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'DrugVsDisease' successfully unpacked and MD5 sums checked
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DrugVsDisease.Rcheck/tests_i386/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("DrugVsDisease")||stop("unable to load DrugVsDisease")
Loading required package: DrugVsDisease
Loading required package: affy
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: biomaRt
Loading required package: ArrayExpress
Loading required package: GEOquery
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: DrugVsDiseasedata
Loading required package: cMap2data
Attaching package: 'cMap2data'
The following object is masked from 'package:DrugVsDiseasedata':
genelist
Loading required package: qvalue
[1] TRUE
> library(BiocGenerics)
> library(RUnit)
> BiocGenerics:::testPackage("DrugVsDisease")
RUNIT TEST PROTOCOL -- Tue Apr 12 18:59:43 2022
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
DrugVsDisease RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
10.57 0.89 11.50
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DrugVsDisease.Rcheck/tests_x64/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> require("DrugVsDisease")||stop("unable to load DrugVsDisease")
Loading required package: DrugVsDisease
Loading required package: affy
Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: limma
Attaching package: 'limma'
The following object is masked from 'package:BiocGenerics':
plotMA
Loading required package: biomaRt
Loading required package: ArrayExpress
Loading required package: GEOquery
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: DrugVsDiseasedata
Loading required package: cMap2data
Attaching package: 'cMap2data'
The following object is masked from 'package:DrugVsDiseasedata':
genelist
Loading required package: qvalue
[1] TRUE
> library(BiocGenerics)
> library(RUnit)
> BiocGenerics:::testPackage("DrugVsDisease")
RUNIT TEST PROTOCOL -- Tue Apr 12 18:59:56 2022
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
DrugVsDisease RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
12.14 0.51 12.64
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DrugVsDisease.Rcheck/examples_i386/DrugVsDisease-Ex.timings
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DrugVsDisease.Rcheck/examples_x64/DrugVsDisease-Ex.timings
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