| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:16 -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 RSVSim package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RSVSim.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 1665/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RSVSim 1.34.0 (landing page) Christoph Bartenhagen
| 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: RSVSim |
| Version: 1.34.0 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RSVSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RSVSim_1.34.0.tar.gz |
| StartedAt: 2022-04-13 02:03:17 -0400 (Wed, 13 Apr 2022) |
| EndedAt: 2022-04-13 02:08:24 -0400 (Wed, 13 Apr 2022) |
| EllapsedTime: 307.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: RSVSim.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RSVSim.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings RSVSim_1.34.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/RSVSim.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 'RSVSim/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RSVSim' version '1.34.0'
* 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 7.2 0.34 7.55
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simulateSV 9.17 0 9.17
* 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/RSVSim.Rcheck/00check.log'
for details.
RSVSim.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/RSVSim_1.34.0.tar.gz && rm -rf RSVSim.buildbin-libdir && mkdir RSVSim.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RSVSim.buildbin-libdir RSVSim_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL RSVSim_1.34.0.zip && rm RSVSim_1.34.0.tar.gz RSVSim_1.34.0.zip
###
##############################################################################
##############################################################################
% 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 353k 100 353k 0 0 419k 0 --:--:-- --:--:-- --:--:-- 419k
100 353k 100 353k 0 0 419k 0 --:--:-- --:--:-- --:--:-- 419k
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_1.34.0.zip
* DONE (RSVSim)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'RSVSim' successfully unpacked and MD5 sums checked
|
RSVSim.Rcheck/examples_i386/RSVSim-Ex.timings
|
RSVSim.Rcheck/examples_x64/RSVSim-Ex.timings
|