John Stansfield
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/multiHiCcompare |
| Branch: RELEASE_3_11 |
| Last Commit: 6522884 |
| Last Changed Date: 2020-04-27 15:18:41 -0400 (Mon, 27 Apr 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-10-17 11:57:13 -0400 (Sat, 17 Oct 2020).
| TO THE DEVELOPERS/MAINTAINERS OF THE multiHiCcompare PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1154/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| multiHiCcompare 1.6.0 John Stansfield
| malbec2 | Linux (Ubuntu 18.04.4 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: multiHiCcompare |
| Version: 1.6.0 |
| Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiHiCcompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings multiHiCcompare_1.6.0.tar.gz |
| StartedAt: 2020-10-17 06:21:06 -0400 (Sat, 17 Oct 2020) |
| EndedAt: 2020-10-17 06:29:41 -0400 (Sat, 17 Oct 2020) |
| EllapsedTime: 515.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: multiHiCcompare.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiHiCcompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings multiHiCcompare_1.6.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/multiHiCcompare.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'multiHiCcompare/DESCRIPTION' ... OK
* this is package 'multiHiCcompare' version '1.6.0'
* package encoding: UTF-8
* 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 'multiHiCcompare' 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
Namespace in Imports field not imported from: 'GenomeInfoDbData'
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
.count_manhattan: no visible global function definition for 'tail'
.count_manhattan: no visible global function definition for 'axis'
.count_manhattan: no visible global function definition for 'textxy'
cyclic_loess: no visible binding for global variable 'chr'
cyclic_loess: no visible binding for global variable 'region1'
cyclic_loess: no visible binding for global variable 'region2'
exportJuicebox: no visible binding for global variable 'logCPM'
exportJuicebox: no visible binding for global variable 'logFC'
exportJuicebox: no visible binding for global variable 'p.adj'
exportJuicebox: no visible global function definition for 'write.table'
fastlo: no visible binding for global variable 'chr'
fastlo: no visible binding for global variable 'region1'
fastlo: no visible binding for global variable 'region2'
hic_exactTest: no visible binding for global variable 'chr'
hic_exactTest: no visible binding for global variable 'region1'
hic_exactTest: no visible binding for global variable 'region2'
hic_filter: no visible binding for global variable 'hg19_cyto'
hic_glm: no visible binding for global variable 'chr'
hic_glm: no visible binding for global variable 'region1'
hic_glm: no visible binding for global variable 'region2'
make_hicexp: no visible binding for global variable 'hg19_cyto'
make_hicexp: no visible binding for global variable 'region2'
make_hicexp: no visible binding for global variable 'region1'
make_hicexp: no visible binding for global variable 'chr'
perm_test: no visible global function definition for 'seqlevelsStyle<-'
perm_test: no visible binding for global variable 'chr'
perm_test: no visible binding for global variable 'start'
perm_test: no visible binding for global variable 'end'
perm_test: no visible global function definition for 'IRanges'
topDirs: no visible binding for global variable 'logCPM'
topDirs: no visible binding for global variable 'logFC'
topDirs: no visible binding for global variable 'p.adj'
topDirs: no visible binding for global variable 'avgLogCPM'
topDirs: no visible binding for global variable 'avgLogFC'
topDirs: no visible binding for global variable 'avgP.adj'
topDirs: no visible binding for global variable 'avgD'
Undefined global functions or variables:
IRanges avgD avgLogCPM avgLogFC avgP.adj axis chr end hg19_cyto
logCPM logFC p.adj region1 region2 seqlevelsStyle<- start tail textxy
write.table
Consider adding
importFrom("graphics", "axis")
importFrom("stats", "end", "start")
importFrom("utils", "tail", "write.table")
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 ... 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
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.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: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.11-bioc/meat/multiHiCcompare.Rcheck/00check.log'
for details.
multiHiCcompare.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/multiHiCcompare_1.6.0.tar.gz && rm -rf multiHiCcompare.buildbin-libdir && mkdir multiHiCcompare.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=multiHiCcompare.buildbin-libdir multiHiCcompare_1.6.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL multiHiCcompare_1.6.0.zip && rm multiHiCcompare_1.6.0.tar.gz multiHiCcompare_1.6.0.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 2555k 100 2555k 0 0 23.7M 0 --:--:-- --:--:-- --:--:-- 25.4M
install for i386
* installing *source* package 'multiHiCcompare' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'multiHiCcompare'
finding HTML links ... done
HCT116_r1 html
HCT116_r2 html
HCT116_r3 html
HCT116_r4 html
HCT116_r5 html
HCT116_r6 html
Hicexp-class html
MD_composite html
MD_hicexp html
cyclic_loess html
exportJuicebox html
fastlo html
hg19_cyto html
hg38_cyto html
hic_exactTest html
hic_filter html
hic_glm html
hic_scale html
hic_table html
hicexp2 html
hicexp_diff html
make_hicexp html
manhattan_hicexp html
meta html
normalized html
perm_test html
plot_counts html
plot_pvals html
pval_heatmap html
resolution html
results html
show html
smartApply html
topDirs 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 'multiHiCcompare' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'multiHiCcompare' as multiHiCcompare_1.6.0.zip
* DONE (multiHiCcompare)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'multiHiCcompare' successfully unpacked and MD5 sums checked
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multiHiCcompare.Rcheck/tests_i386/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.
> library(testthat)
> library(multiHiCcompare)
>
> test_check("multiHiCcompare")
== testthat results ===========================================================
[ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
50.62 1.87 52.46
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multiHiCcompare.Rcheck/tests_x64/testthat.Rout
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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.
> library(testthat)
> library(multiHiCcompare)
>
> test_check("multiHiCcompare")
== testthat results ===========================================================
[ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
53.79 1.07 54.71
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multiHiCcompare.Rcheck/examples_i386/multiHiCcompare-Ex.timings
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multiHiCcompare.Rcheck/examples_x64/multiHiCcompare-Ex.timings
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