Benjamin Johnson
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/compartmap |
| Branch: RELEASE_3_8 |
| Last Commit: fd8e478 |
| Last Changed Date: 2019-01-04 13:25:53 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-13 11:29:55 -0400 (Sat, 13 Apr 2019).
| Package 309/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| compartmap 1.0.3 Benjamin Johnson
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ WARNINGS ] | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |
| Package: compartmap |
| Version: 1.0.3 |
| Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compartmap.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings compartmap_1.0.3.tar.gz |
| StartedAt: 2019-04-13 01:24:40 -0400 (Sat, 13 Apr 2019) |
| EndedAt: 2019-04-13 01:33:41 -0400 (Sat, 13 Apr 2019) |
| EllapsedTime: 541.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: compartmap.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:compartmap.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings compartmap_1.0.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/compartmap.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 'compartmap/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'compartmap' version '1.0.3'
* package encoding: UTF-8
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'compartmap' 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
package 'methods' is used but not declared
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.arraycompartments: no visible global function definition for
'seqlevels'
.createCorMatrix: no visible global function definition for 'seqlevels'
.createCorMatrix: no visible global function definition for
'seqlevels<-'
.createCorMatrix: no visible global function definition for 'cor'
.extractAB: no visible global function definition for 'cor'
.extractAB: no visible global function definition for 'colSums2'
.fsvd: no visible global function definition for 'rnorm'
.getFirstPC: no visible global function definition for 'cor'
.getFirstPCarray: no visible global function definition for 'rowMeans2'
.getPairedAllChrsArray: no visible global function definition for
'seqlevels'
.removeBadBins: no visible global function definition for 'colAlls'
.returnBinnedMatrix : bin2D: no visible global function definition for
'median'
.returnBinnedMatrix: no visible global function definition for
'seqlengths'
.returnBinnedMatrix: no visible global function definition for
'standardChromosomes'
.returnBinnedMatrix: no visible global function definition for
'seqlengths<-'
.returnBinnedMatrix: no visible global function definition for
'seqlevels'
.returnBinnedMatrix: no visible global function definition for
'subjectHits'
.run_examples: no visible global function definition for 'data'
.run_examples: no visible binding for global variable
'bulkATAC_raw_filtered_chr14'
.run_examples: no visible binding for global variable
'filtered.data.chr14'
.run_examples: no visible binding for global variable
'meth_array_450k_chr14'
.run_examples: no visible binding for global variable
'array.data.chr14'
.unitarize: no visible global function definition for 'median'
getBinMatrix: no visible global function definition for 'seqlengths'
getBinMatrix: no visible global function definition for 'IRanges'
getCompartments: no visible global function definition for 'seqlevels'
getCorMatrix: no visible global function definition for 'cor'
plotAB: no visible global function definition for 'barplot'
Undefined global functions or variables:
IRanges array.data.chr14 barplot bulkATAC_raw_filtered_chr14 colAlls
colSums2 cor data filtered.data.chr14 median meth_array_450k_chr14
rnorm rowMeans2 seqlengths seqlengths<- seqlevels seqlevels<-
standardChromosomes subjectHits
Consider adding
importFrom("graphics", "barplot")
importFrom("stats", "cor", "median", "rnorm")
importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'getABSignal':
getABSignal
Code: function(x, k = 2, iter = 2, squeeze = FALSE)
Docs: function(x, k = 5, iter = 2, squeeze = FALSE)
Mismatches in argument default values:
Name: 'k' Code: 2 Docs: 5
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getATACABsignal 17.30 0.97 18.28
getCompartments 12.56 0.48 13.05
getABSignal 5.19 0.75 5.94
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
getATACABsignal 16.69 0.61 17.30
getCompartments 14.26 0.42 14.68
* 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: 1 WARNING, 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.8-bioc/meat/compartmap.Rcheck/00check.log'
for details.
compartmap.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/compartmap_1.0.3.tar.gz && rm -rf compartmap.buildbin-libdir && mkdir compartmap.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=compartmap.buildbin-libdir compartmap_1.0.3.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL compartmap_1.0.3.zip && rm compartmap_1.0.3.tar.gz compartmap_1.0.3.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
0 3081k 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 3081k 100 3081k 0 0 28.5M 0 --:--:-- --:--:-- --:--:-- 29.5M
install for i386
* installing *source* package 'compartmap' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'compartmap'
finding HTML links ... done
array.data.chr14 html
filtered.data.chr14 html
fisherZ html
getABSignal html
getATACABsignal html
getArrayABsignal html
getBinMatrix html
getCompartments html
getCorMatrix html
ifisherZ html
plotAB html
** building package indices
** installing vignettes
'compartmap_vignette.Rmd' using 'UTF-8'
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'compartmap' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'compartmap' as compartmap_1.0.3.zip
* DONE (compartmap)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'compartmap' successfully unpacked and MD5 sums checked
In R CMD INSTALL
|
compartmap.Rcheck/examples_i386/compartmap-Ex.timings
|
compartmap.Rcheck/examples_x64/compartmap-Ex.timings
|