Nicolas Servant
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/HiTC |
| Branch: RELEASE_3_8 |
| Last Commit: be108ad |
| Last Changed Date: 2018-10-30 11:41:49 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:22:08 -0400 (Sat, 13 Apr 2019).
| Package 729/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| HiTC 1.26.0 Nicolas Servant
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: HiTC |
| Version: 1.26.0 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HiTC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings HiTC_1.26.0.tar.gz |
| StartedAt: 2019-04-13 03:03:37 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 03:10:26 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 408.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HiTC.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:HiTC.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings HiTC_1.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/HiTC.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HiTC/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HiTC' version '1.26.0'
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'HiTC' 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
directionalityIndex: no visible global function definition for
'subjectHits'
directionalityIndex: no visible global function definition for
'queryHits'
getBlocsIndex: no visible global function definition for 'Rle'
getExpectedCountsMean: no visible global function definition for 'Rle'
normLGF: no visible global function definition for 'glm.nb'
slidingWindow: no visible binding for global variable 'consV'
splitCombinedContacts : <anonymous>: no visible global function
definition for 'seqlevels<-'
divide,HTCexp-HTCexp: no visible global function definition for
'queryHits'
divide,HTCexp-HTCexp: no visible global function definition for
'subjectHits'
isBinned,HTCexp: no visible global function definition for
'countMatches'
substract,HTCexp-HTCexp: no visible global function definition for
'queryHits'
substract,HTCexp-HTCexp: no visible global function definition for
'subjectHits'
Undefined global functions or variables:
Rle consV countMatches glm.nb queryHits seqlevels<- subjectHits
* 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 or elapsed time > 5s
user system elapsed
directionalityIndex 46.61 0.53 48.42
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
directionalityIndex 40.42 0.42 40.85
CQC 5.02 0.17 5.19
* 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-3.8-bioc/meat/HiTC.Rcheck/00check.log'
for details.
HiTC.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/HiTC_1.26.0.tar.gz && rm -rf HiTC.buildbin-libdir && mkdir HiTC.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=HiTC.buildbin-libdir HiTC_1.26.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL HiTC_1.26.0.zip && rm HiTC_1.26.0.tar.gz HiTC_1.26.0.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 722k 100 722k 0 0 17.8M 0 --:--:-- --:--:-- --:--:-- 19.6M
install for i386
* installing *source* package 'HiTC' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'HiTC'
finding HTML links ... done
CQC html
HTCexp-class html
HTClist-class html
HiTC-internal html
Nora_5C html
binningC html
directionalityIndex html
discretize html
export.my5C html
exportC html
extractRegion html
getAnnotatedRestrictionSites html
getExpectedCounts html
getPearsonMap html
getRestrictionFragmentsPerChromosome html
import.my5C html
importC html
intervalsDist html
mapC html
normICE html
normLGF html
pca.hic html
removeIntervals html
setGenomicFeatures html
setIntervalScale html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'HiTC' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HiTC' as HiTC_1.26.0.zip
* DONE (HiTC)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'HiTC' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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HiTC.Rcheck/examples_i386/HiTC-Ex.timings
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HiTC.Rcheck/examples_x64/HiTC-Ex.timings
|