HiCcompare 0.99.13
John Stansfield
| Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/HiCcompare | | Last Changed Rev: 131538 / Revision: 131943 | | Last Changed Date: 2017-07-24 16:34:21 -0400 (Mon, 24 Jul 2017) |
| 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 | |
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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_0.99.13.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_0.99.13.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/HiCcompare.Rcheck'
* using R version 3.4.1 (2017-06-30)
* 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 '0.99.13'
* 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 ... 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
** 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'
.loess.as: no visible global function definition for 'lines'
.loess.as: no visible global function definition for 'persp'
.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'
.sim.mat: no visible global function definition for 'head'
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 global function definition for 'is'
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_diff: no visible global function definition for 'is'
hic_simulate: no visible binding for global variable 'bias.slope'
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'
Undefined global functions or variables:
D IF IF1 IF2 M adj.IF1 adj.IF2 adj.M bias.slope chr1 chr2 fold.change
head i is j lines p.adj p.value persp region1 region2
Consider adding
importFrom("graphics", "lines", "persp")
importFrom("methods", "is")
importFrom("stats", "D")
importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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
hic_simulate 21.52 0.07 21.58
sim.other.methods 18.31 0.02 18.33
hic_diff 7.80 0.20 8.00
MD.plot2 6.11 0.02 6.12
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
hic_simulate 18.43 0.01 18.52
sim.other.methods 16.31 0.00 16.31
MD.plot2 5.60 0.05 5.69
hic_diff 5.05 0.04 5.08
* 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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.6-bioc/meat/HiCcompare.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'HiCcompare' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'HiCcompare' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HiCcompare' as HiCcompare_0.99.13.zip
* DONE (HiCcompare)