Christoph Bartenhagen
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/RSVSim |
| Branch: RELEASE_3_12 |
| Last Commit: cfe4d5f |
| Last Changed Date: 2020-10-27 10:48:38 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:33:22 -0400 (Thu, 06 May 2021).
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To the developers/maintainers of the RSVSim package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1587/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RSVSim 1.30.0 (landing page) Christoph Bartenhagen
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: RSVSim |
| Version: 1.30.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RSVSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RSVSim_1.30.0.tar.gz |
| StartedAt: 2021-05-06 06:29:03 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 06:33:51 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 288.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RSVSim.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RSVSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings RSVSim_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/RSVSim.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RSVSim/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RSVSim' version '1.30.0'
* 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 'RSVSim' 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 in package code:
'BSgenome.Hsapiens.UCSC.hg19' 'BSgenome.Hsapiens.UCSC.hg19.masked'
'MASS' 'rtracklayer'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'methods'
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
.drawPos: no visible global function definition for 'seqlevels'
.drawPos: no visible global function definition for 'queryHits'
.getHG19: no visible binding for global variable
'BSgenome.Hsapiens.UCSC.hg19.masked'
.getHG19: no visible binding for global variable 'Hsapiens'
.getHG19: no visible global function definition for 'as'
.getSVSizes: no visible global function definition for 'rbeta'
.loadFromBSGenome_TandemRepeats: no visible binding for global variable
'BSgenome.Hsapiens.UCSC.hg19.masked'
.loadFromBSGenome_TandemRepeats: no visible global function definition
for 'seqlevels<-'
.loadFromBSGenome_TandemRepeats: no visible global function definition
for 'as'
.loadFromUCSC_RepeatMasks: no visible global function definition for
'browserSession'
.loadFromUCSC_RepeatMasks: no visible global function definition for
'genome<-'
.loadFromUCSC_RepeatMasks: no visible global function definition for
'ucscTableQuery'
.loadFromUCSC_RepeatMasks: no visible global function definition for
'txtProgressBar'
.loadFromUCSC_RepeatMasks: no visible global function definition for
'range<-'
.loadFromUCSC_RepeatMasks: no visible global function definition for
'getTable'
.loadFromUCSC_RepeatMasks: no visible global function definition for
'setTxtProgressBar'
.loadFromUCSC_RepeatMasks: no visible global function definition for
'data'
.loadFromUCSC_SegDups: no visible global function definition for
'browserSession'
.loadFromUCSC_SegDups: no visible global function definition for
'genome<-'
.loadFromUCSC_SegDups: no visible global function definition for
'getTable'
.loadFromUCSC_SegDups: no visible global function definition for
'ucscTableQuery'
.readRepeatMaskerOutput: no visible global function definition for
'read.table'
.readRepeatMaskerOutput: no visible global function definition for
'data'
.simInsertionPositions: no visible global function definition for
'txtProgressBar'
.simInsertionPositions: no visible global function definition for
'seqlevels'
.simInsertionPositions: no visible global function definition for
'setTxtProgressBar'
.simPositions: no visible global function definition for
'txtProgressBar'
.simPositions: no visible global function definition for
'setTxtProgressBar'
.simTranslocationPositions: no visible global function definition for
'txtProgressBar'
.simTranslocationPositions: no visible global function definition for
'seqlevels'
.simTranslocationPositions: no visible global function definition for
'setTxtProgressBar'
.subtractIntervals: no visible global function definition for
'seqlevels<-'
.testSVSim: no visible global function definition for 'metadata'
compareSV,character-character: no visible global function definition
for 'read.table'
compareSV,character-data.frame: no visible global function definition
for 'read.table'
estimateSVSizes,numeric-numeric-ANY-ANY-missing: no visible global
function definition for 'fitdistr'
simulateSV,ANY: no visible global function definition for 'data'
simulateSV,ANY: no visible global function definition for
'txtProgressBar'
simulateSV,ANY: no visible global function definition for
'setTxtProgressBar'
simulateSV,ANY: no visible global function definition for 'write.table'
simulateSV,ANY: no visible global function definition for 'metadata<-'
Undefined global functions or variables:
BSgenome.Hsapiens.UCSC.hg19.masked Hsapiens as browserSession data
fitdistr genome<- getTable metadata metadata<- queryHits range<-
rbeta read.table seqlevels seqlevels<- setTxtProgressBar
txtProgressBar ucscTableQuery write.table
Consider adding
importFrom("methods", "as")
importFrom("stats", "rbeta")
importFrom("utils", "data", "read.table", "setTxtProgressBar",
"txtProgressBar", "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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simulateSV 11.05 0.37 11.47
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simulateSV 9.42 0.00 9.42
compareSVs 5.24 0.11 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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/RSVSim.Rcheck/00check.log'
for details.
RSVSim.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/RSVSim_1.30.0.tar.gz && rm -rf RSVSim.buildbin-libdir && mkdir RSVSim.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RSVSim.buildbin-libdir RSVSim_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL RSVSim_1.30.0.zip && rm RSVSim_1.30.0.tar.gz RSVSim_1.30.0.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
100 351k 100 351k 0 0 16.0M 0 --:--:-- --:--:-- --:--:-- 17.1M
install for i386
* installing *source* package 'RSVSim' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'RSVSim'
finding HTML links ... done
compareSVs html
estimateSVSizes html
segmentalDuplications html
simulateSV html
weightsMechanisms html
weightsRepeats 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 'RSVSim' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RSVSim' as RSVSim_1.30.0.zip
* DONE (RSVSim)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'RSVSim' successfully unpacked and MD5 sums checked
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RSVSim.Rcheck/examples_i386/RSVSim-Ex.timings
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RSVSim.Rcheck/examples_x64/RSVSim-Ex.timings
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