Kun Liang
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/DBChIP |
| Branch: RELEASE_3_12 |
| Last Commit: a165505 |
| Last Changed Date: 2020-10-27 10:46:27 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:30:36 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the DBChIP package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 428/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| DBChIP 1.34.0 (landing page) Kun Liang
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: DBChIP |
| Version: 1.34.0 |
| Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DBChIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DBChIP_1.34.0.tar.gz |
| StartedAt: 2021-05-06 01:59:24 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 02:02:21 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 176.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: DBChIP.Rcheck |
| Warnings: 1 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DBChIP.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings DBChIP_1.34.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/DBChIP.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DBChIP/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DBChIP' version '1.34.0'
* 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 'DBChIP' can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/DBChIP.Rcheck/00install.out' for details.
* 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
'library' or 'require' calls to packages already attached by Depends:
'DESeq' 'edgeR'
Please remove these calls from your code.
'library' or 'require' call to 'ShortRead' in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
bin.data: no visible global function definition for 'hist'
comp.bkg.size : <anonymous>: no visible global function definition for
'hist'
est.common.disp.by.collapse: no visible global function definition for
'combn'
est.common.disp.by.collapse: no visible global function definition for
'model.matrix'
est.common.disp.by.collapse: no visible global function definition for
'quantile'
get.chr.site.count: no visible global function definition for 'hist'
get.chr.unique.read.count: no visible global function definition for
'hist'
get.cluster: no visible global function definition for 'dist'
get.cluster: no visible global function definition for 'hclust'
get.cluster: no visible global function definition for 'cutree'
get.cluster: no visible global function definition for 'weighted.mean'
get.coverage: no visible global function definition for 'hist'
get.coverage: no visible global function definition for 'convolve'
median.ratio : <anonymous>: no visible global function definition for
'median'
read.AlignedRead: no visible global function definition for 'is'
read.AlignedRead: no visible global function definition for 'position'
read.AlignedRead: no visible global function definition for 'strand'
read.AlignedRead: no visible global function definition for 'width'
read.AlignedRead: no visible global function definition for
'chromosome'
read.BED: no visible global function definition for 'read.delim'
single.peak: no visible global function definition for 'par'
single.peak: no visible global function definition for 'matplot'
single.peak: no visible global function definition for 'abline'
single.peak: no visible global function definition for 'mtext'
site.merge : <anonymous>: no visible global function definition for
'weighted.mean'
test.diff.binding.2sample : <anonymous>: no visible global function
definition for 'binom.test'
test.diff.binding.DESeq: no visible global function definition for
'pData'
test.diff.binding.DESeq: no visible global function definition for
'pData<-'
test.diff.binding.edgeR: no visible global function definition for
'model.matrix'
Undefined global functions or variables:
abline binom.test chromosome combn convolve cutree dist hclust hist
is matplot median model.matrix mtext pData pData<- par position
quantile read.delim strand weighted.mean width
Consider adding
importFrom("graphics", "abline", "hist", "matplot", "mtext", "par")
importFrom("methods", "is")
importFrom("stats", "binom.test", "convolve", "cutree", "dist",
"hclust", "median", "model.matrix", "quantile",
"weighted.mean")
importFrom("utils", "combn", "read.delim")
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 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 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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
'C:/Users/biocbuild/bbs-3.12-bioc/meat/DBChIP.Rcheck/00check.log'
for details.
DBChIP.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/DBChIP_1.34.0.tar.gz && rm -rf DBChIP.buildbin-libdir && mkdir DBChIP.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DBChIP.buildbin-libdir DBChIP_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL DBChIP_1.34.0.zip && rm DBChIP_1.34.0.tar.gz DBChIP_1.34.0.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 1747k 100 1747k 0 0 16.3M 0 --:--:-- --:--:-- --:--:-- 16.5M
install for i386
* installing *source* package 'DBChIP' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'DESeq' is deprecated and will be removed from Bioconductor
version 3.13. Please use DESeq2
** help
*** installing help indices
converting help for package 'DBChIP'
finding HTML links ... done
DBChIP-package html
DBChIP html
PHA4 html
binding.site.list html
chip.data.list html
conds html
get.site.count html
input.data.list html
load.data html
plotPeak html
read.binding.site.list html
report.peak html
site.merge html
test.diff.binding html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
version 3.13. Please use DESeq2
** testing if installed package can be loaded from final location
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
version 3.13. Please use DESeq2
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'DBChIP' ...
** testing if installed package can be loaded
Warning: Package 'DESeq' is deprecated and will be removed from Bioconductor
version 3.13. Please use DESeq2
* MD5 sums
packaged installation of 'DBChIP' as DBChIP_1.34.0.zip
* DONE (DBChIP)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'DBChIP' successfully unpacked and MD5 sums checked
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DBChIP.Rcheck/tests_i386/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.
> require("DBChIP") || stop("unable to load DBChIP")
Loading required package: DBChIP
Loading required package: edgeR
Loading required package: limma
Loading required package: DESeq
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:limma':
plotMA
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: locfit
locfit 1.5-9.4 2020-03-24
Loading required package: lattice
[1] TRUE
Warning message:
Package 'DESeq' is deprecated and will be removed from Bioconductor
version 3.13. Please use DESeq2
> BiocGenerics:::testPackage("DBChIP")
merging sites from different conditions to consensus sites.done
reading data...done
computing normalization factor between ChIP and control samples.done
count ChIP reads around each binding site.done
RUNIT TEST PROTOCOL -- Thu May 06 02:02:08 2021
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
DBChIP RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
7.09 0.34 7.45
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DBChIP.Rcheck/tests_x64/runTests.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.
> require("DBChIP") || stop("unable to load DBChIP")
Loading required package: DBChIP
Loading required package: edgeR
Loading required package: limma
Loading required package: DESeq
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from 'package:limma':
plotMA
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: locfit
locfit 1.5-9.4 2020-03-24
Loading required package: lattice
[1] TRUE
Warning message:
Package 'DESeq' is deprecated and will be removed from Bioconductor
version 3.13. Please use DESeq2
> BiocGenerics:::testPackage("DBChIP")
merging sites from different conditions to consensus sites.done
reading data...done
computing normalization factor between ChIP and control samples.done
count ChIP reads around each binding site.done
RUNIT TEST PROTOCOL -- Thu May 06 02:02:16 2021
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
DBChIP RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
7.51 0.34 7.84
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DBChIP.Rcheck/examples_i386/DBChIP-Ex.timings
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DBChIP.Rcheck/examples_x64/DBChIP-Ex.timings
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