John Stansfield
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/multiHiCcompare |
| Branch: RELEASE_3_9 |
| Last Commit: 1ac2fa1 |
| Last Changed Date: 2019-05-02 11:54:12 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:42:07 -0400 (Wed, 16 Oct 2019).
| Package 1067/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| multiHiCcompare 1.2.0 John Stansfield
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: multiHiCcompare |
| Version: 1.2.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiHiCcompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings multiHiCcompare_1.2.0.tar.gz |
| StartedAt: 2019-10-16 05:28:40 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 05:36:43 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 482.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: multiHiCcompare.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:multiHiCcompare.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings multiHiCcompare_1.2.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/multiHiCcompare.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.2.0'
* 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-3.9-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/3.9/bioc/src/contrib/multiHiCcompare_1.2.0.tar.gz && rm -rf multiHiCcompare.buildbin-libdir && mkdir multiHiCcompare.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=multiHiCcompare.buildbin-libdir multiHiCcompare_1.2.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL multiHiCcompare_1.2.0.zip && rm multiHiCcompare_1.2.0.tar.gz multiHiCcompare_1.2.0.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 2556k 100 2556k 0 0 12.2M 0 --:--:-- --:--:-- --:--:-- 12.6M
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_1.2.0.zip
* DONE (multiHiCcompare)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'multiHiCcompare' successfully unpacked and MD5 sums checked
|
multiHiCcompare.Rcheck/tests_i386/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
deprecated and future versions of Bioconductor may not have it
available. Users who want more current data are encouraged to look
at the KEGGREST or reactome.db packages
>
> test_check("multiHiCcompare")
== testthat results ===========================================================
[ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
49.26 1.64 50.84
|
multiHiCcompare.Rcheck/tests_x64/testthat.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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)
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
deprecated and future versions of Bioconductor may not have it
available. Users who want more current data are encouraged to look
at the KEGGREST or reactome.db packages
>
> test_check("multiHiCcompare")
== testthat results ===========================================================
[ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
45.01 0.90 45.62
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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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