John Stansfield
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/HiCcompare |
| Branch: RELEASE_3_6 |
| Last Commit: 5b3933b |
| Last Changed Date: 2017-10-30 12:41:33 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:30:11 -0400 (Thu, 12 Apr 2018).
| Package 650/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| HiCcompare 1.0.0 John Stansfield
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | [ OK ] | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: HiCcompare |
| Version: 1.0.0 |
| Command: rm -rf HiCcompare.buildbin-libdir HiCcompare.Rcheck && mkdir HiCcompare.buildbin-libdir HiCcompare.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HiCcompare.buildbin-libdir HiCcompare_1.0.0.tar.gz >HiCcompare.Rcheck\00install.out 2>&1 && cp HiCcompare.Rcheck\00install.out HiCcompare-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=HiCcompare.buildbin-libdir --install="check:HiCcompare-install.out" --force-multiarch --no-vignettes --timings HiCcompare_1.0.0.tar.gz |
| StartedAt: 2018-04-12 00:42:39 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:50:31 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 472.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: HiCcompare.Rcheck |
| Warnings: 0 |
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### Running command:
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### rm -rf HiCcompare.buildbin-libdir HiCcompare.Rcheck && mkdir HiCcompare.buildbin-libdir HiCcompare.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HiCcompare.buildbin-libdir HiCcompare_1.0.0.tar.gz >HiCcompare.Rcheck\00install.out 2>&1 && cp HiCcompare.Rcheck\00install.out HiCcompare-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=HiCcompare.buildbin-libdir --install="check:HiCcompare-install.out" --force-multiarch --no-vignettes --timings HiCcompare_1.0.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/HiCcompare.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HiCcompare/DESCRIPTION' ... OK
* this is package 'HiCcompare' version '1.0.0'
* 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 'HiCcompare' can be installed ... OK
* checking installed package size ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
data 5.6Mb
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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
.calc.pval: no visible binding for global variable 'D'
.calc.pval: no visible binding for global variable 'p.value'
.calc.pval: no visible binding for global variable 'p.adj'
.calc.pval: no visible binding for global variable 'adj.M'
.calc.pval: no visible binding for global variable 'fold.change'
.calc.pval: no visible binding for global variable 'adj.IF2'
.calc.pval: no visible binding for global variable 'adj.IF1'
.internal_weight_M: no visible binding for global variable 'A'
.internal_weight_M: no visible binding for global variable 'adj.IF1'
.internal_weight_M: no visible binding for global variable 'adj.IF2'
.internal_weight_M: no visible binding for global variable 'adj.M'
.loess.matrix: no visible binding for global variable 'adj.IF1'
.loess.matrix: no visible binding for global variable 'IF1'
.loess.matrix: no visible binding for global variable 'adj.IF2'
.loess.matrix: no visible binding for global variable 'IF2'
.loess.matrix: no visible binding for global variable 'adj.M'
.split_cent: no visible binding for global variable
'centromere_locations'
.split_cent: no visible binding for global variable 'start1'
.split_cent: no visible binding for global variable 'start2'
.split_cent: no visible binding for global variable 'chr1'
.split_cent: no visible binding for global variable 'chr2'
MA_norm: no visible binding for global variable 'D'
MA_norm: no visible binding for global variable 'M'
MA_norm: no visible binding for global variable 'adj.IF1'
MA_norm: no visible binding for global variable 'IF1'
MA_norm: no visible binding for global variable 'adj.IF2'
MA_norm: no visible binding for global variable 'IF2'
MA_norm: no visible binding for global variable 'adj.M'
cooler2sparse: no visible binding for global variable 'chr1'
cooler2sparse: no visible binding for global variable 'chr2'
cooler2sparse: no visible binding for global variable 'IF'
create.hic.table: no visible binding for global variable 'D'
create.hic.table: no visible binding for global variable 'region2'
create.hic.table: no visible binding for global variable 'region1'
create.hic.table: no visible binding for global variable 'IF2'
create.hic.table: no visible binding for global variable 'M'
create.hic.table: no visible binding for global variable 'IF1'
create.hic.table: no visible binding for global variable 'i'
create.hic.table: no visible binding for global variable 'j'
full2sparse: no visible binding for global variable 'IF'
hic_simulate: no visible binding for global variable 'bias.slope'
hicpro2bedpe: no visible binding for global variable 'chr1'
hicpro2bedpe: no visible binding for global variable 'chr2'
plot_A : <anonymous>: no visible binding for global variable 'adj.IF1'
plot_A : <anonymous>: no visible binding for global variable 'adj.IF2'
sim.other.methods: no visible binding for global variable 'adj.IF1'
sim.other.methods: no visible binding for global variable 'IF1'
sim.other.methods: no visible binding for global variable 'adj.IF2'
sim.other.methods: no visible binding for global variable 'IF2'
sim.other.methods: no visible binding for global variable 'adj.M'
sim.other.methods: no visible binding for global variable 'M'
total_sum: no visible binding for global variable 'IF2'
total_sum: no visible binding for global variable 'M'
total_sum: no visible binding for global variable 'IF1'
total_sum: no visible binding for global variable 'chr1'
volcano: no visible binding for global variable 'A'
volcano: no visible binding for global variable 'adj.IF1'
volcano: no visible binding for global variable 'adj.IF2'
volcano: no visible binding for global variable 'p.value'
volcano: no visible binding for global variable 'D'
Undefined global functions or variables:
A D IF IF1 IF2 M adj.IF1 adj.IF2 adj.M bias.slope
centromere_locations chr1 chr2 fold.change i j p.adj p.value region1
region2 start1 start2
Consider adding
importFrom("stats", "D")
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 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
sim.other.methods 16.69 0.08 16.77
hic_simulate 16.63 0.11 16.73
MD.plot2 6.49 0.01 6.50
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
sim.other.methods 14.33 0.05 14.37
hic_simulate 13.52 0.00 13.53
MD.plot2 5.03 0.03 5.07
hic_diff 3.75 0.00 6.13
* 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-3.6-bioc/meat/HiCcompare.Rcheck/00check.log'
for details.
HiCcompare.Rcheck/00install.out
install for i386
* installing *source* package 'HiCcompare' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'HiCcompare'
finding HTML links ... done
HMEC.chr10 html
HMEC.chr22 html
HiCcompare-package html
KRnorm html
MA_norm html
MD.plot1 html
MD.plot2 html
NHEK.chr10 html
NHEK.chr22 html
SCN html
brain_table html
centromere_locations html
cooler html
cooler2sparse html
create.hic.table html
full2sparse html
get_CNV html
hg19_blacklist html
hg38_blacklist html
hic_diff html
hic_loess html
hic_simulate html
hicpro2bedpe html
hmec.IS html
make_InteractionSet html
nhek.IS html
plot_A html
remove_centromere html
sim.other.methods html
sparse2full html
split_centromere html
total_sum html
visualize_pvals html
weight_M html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'HiCcompare' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HiCcompare' as HiCcompare_1.0.0.zip
* DONE (HiCcompare)
In R CMD INSTALL
In R CMD INSTALL
|
HiCcompare.Rcheck/tests_i386/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(HiCcompare)
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
>
> test_check("HiCcompare")
== testthat results ===========================================================
OK: 27 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
44.29 0.32 44.60
|
HiCcompare.Rcheck/tests_x64/testthat.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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(HiCcompare)
Loading required package: dplyr
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
>
> test_check("HiCcompare")
== testthat results ===========================================================
OK: 27 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
34.23 0.39 34.62
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HiCcompare.Rcheck/examples_i386/HiCcompare-Ex.timings
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HiCcompare.Rcheck/examples_x64/HiCcompare-Ex.timings
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