| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:33 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the HiCcompare package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 891/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HiCcompare 1.21.0 (landing page) John Stansfield
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
| Package: HiCcompare |
| Version: 1.21.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCcompare.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings HiCcompare_1.21.0.tar.gz |
| StartedAt: 2022-12-29 00:28:59 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 00:32:13 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 194.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HiCcompare.Rcheck |
| Warnings: 1 |
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### Running command:
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### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HiCcompare.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings HiCcompare_1.21.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/HiCcompare.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'HiCcompare/DESCRIPTION' ... OK
* this is package 'HiCcompare' version '1.21.0'
* 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 5.9Mb
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
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.adjust_pval : <anonymous>: no visible binding for global variable
'p.adj'
.adjust_pval : <anonymous>: no visible binding for global variable
'p.value'
.adjust_pval: no visible binding for global variable 'p.value'
.adjust_pval: no visible binding for global variable 'p.adj'
.calc.diff.thresh: no visible global function definition for 'sd'
.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'
.calc_z2: no visible global function definition for 'sd'
.calc_z2: no visible binding for global variable 'Z'
.calc_z2: no visible global function definition for 'pnorm'
.calc_z2: no visible binding for global variable 'p.value'
.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'
.loess.matrix: no visible binding for global variable 'A'
.sim.mat: no visible global function definition for 'head'
.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'
filter_params: no visible binding for global variable 'M'
filter_params: no visible binding for global variable 'IF1'
filter_params: no visible binding for global variable 'IF2'
filter_params: no visible global function definition for 'axis'
full2sparse: no visible binding for global variable 'IF'
hic_compare : <anonymous>: no visible binding for global variable
'p.adj'
hic_simulate: no visible binding for global variable 'bias.slope'
hic_simulate: no visible global function definition for 'na.omit'
hicpro2bedpe: no visible binding for global variable 'chr1'
hicpro2bedpe: no visible binding for global variable 'chr2'
manhattan_plot: no visible binding for global variable 'bp'
manhattan_plot: no visible binding for global variable 'count'
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'
sim.other.methods: no visible global function definition for 'na.omit'
sim_matrix: no visible binding for global variable 'bias.slope'
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 Z adj.IF1 adj.IF2 adj.M axis bias.slope bp
centromere_locations chr1 chr2 count fold.change head i j na.omit
p.adj p.value pnorm region1 region2 sd start1 start2
Consider adding
importFrom("graphics", "axis")
importFrom("stats", "D", "na.omit", "pnorm", "sd")
importFrom("utils", "head")
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 LazyData ... WARNING
LazyData DB of 5.6 MB without LazyDataCompression set
See ยง1.1.6 of 'Writing R Extensions'
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
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 WARNING, 2 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/HiCcompare.Rcheck/00check.log'
for details.
HiCcompare.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL HiCcompare ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'HiCcompare' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to 'ceiling' ** help *** installing help indices ** 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 * DONE (HiCcompare)
HiCcompare.Rcheck/tests/testthat.Rout
R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 28 ]
>
> proc.time()
user system elapsed
8.12 0.56 9.48
HiCcompare.Rcheck/HiCcompare-Ex.timings
| name | user | system | elapsed | |
| KRnorm | 0 | 0 | 0 | |
| MA_norm | 0.07 | 0.02 | 0.09 | |
| MD.plot1 | 0.68 | 0.00 | 0.67 | |
| MD.plot2 | 0.20 | 0.00 | 0.21 | |
| SCN | 0 | 0 | 0 | |
| cooler2bedpe | 0 | 0 | 0 | |
| cooler2sparse | 0.58 | 0.08 | 0.65 | |
| create.hic.table | 0.01 | 0.00 | 0.02 | |
| filter_params | 2.52 | 0.12 | 2.64 | |
| full2sparse | 0 | 0 | 0 | |
| get_CNV | 0 | 0 | 0 | |
| hic_compare | 0.30 | 0.02 | 0.31 | |
| hic_diff | 3.12 | 0.70 | 3.83 | |
| hic_loess | 0.17 | 0.03 | 0.20 | |
| hic_simulate | 0.84 | 0.00 | 0.86 | |
| hicpro2bedpe | 0 | 0 | 0 | |
| make_InteractionSet | 0.13 | 0.02 | 0.14 | |
| manhattan_plot | 0.42 | 0.03 | 0.45 | |
| remove_centromere | 0 | 0 | 0 | |
| sim.other.methods | 0.56 | 0.00 | 0.56 | |
| sim_matrix | 0.83 | 0.00 | 0.83 | |
| sparse2full | 0 | 0 | 0 | |
| split_centromere | 0.00 | 0.01 | 0.01 | |
| total_sum | 0.09 | 0.02 | 0.13 | |
| visualize_pvals | 0.50 | 0.02 | 0.51 | |