| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:37 -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 metagene package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1131/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metagene 2.31.0 (landing page) Charles Joly Beauparlant
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
| Package: metagene |
| Version: 2.31.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metagene.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings metagene_2.31.0.tar.gz |
| StartedAt: 2022-12-29 01:11:32 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 01:16:16 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 284.0 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: metagene.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:metagene.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings metagene_2.31.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/metagene.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 'metagene/DESCRIPTION' ... OK
* this is package 'metagene' version '2.31.0'
* 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 'metagene' can be installed ... OK
* checking installed package size ... NOTE
installed size is 7.1Mb
sub-directories of 1Mb or more:
extdata 5.4Mb
* 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
NCIS.internal: no visible global function definition for
'est.norm.med.search'
avoid_gaps_update: no visible binding for global variable 'value'
avoid_gaps_update: no visible binding for global variable 'bam'
avoid_gaps_update: no visible binding for global variable 'tab'
avoid_gaps_update: no visible binding for global variable 'nuc'
bin.data: no visible global function definition for 'hist'
permutation_test: no visible global function definition for '.'
permutation_test: no visible binding for global variable 'value'
plot_metagene: no visible binding for global variable 'bin'
plot_metagene: no visible binding for global variable 'value'
plot_metagene: no visible binding for global variable 'qinf'
plot_metagene: no visible binding for global variable 'qsup'
plot_metagene: no visible binding for global variable 'group'
plot_metagene: no visible binding for global variable 'nuc'
plot_metagene: no visible binding for global variable 'design'
plot_metagene: no visible binding for global variable 'nuctot'
Undefined global functions or variables:
. bam bin design est.norm.med.search group hist nuc nuctot qinf qsup
tab value
Consider adding
importFrom("graphics", "hist")
to your NAMESPACE file.
* checking Rd files ... WARNING
checkRd: (5) Bam_Handler.Rd:22: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:42: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:46: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:50: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:54: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:58: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:61-62: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:71-72: \item in \describe must have non-empty label
checkRd: (5) Bam_Handler.Rd:81: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:23-26: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:61-62: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:77-78: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:102-103: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:116: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:119: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:122: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:127: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:130: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:133: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:144: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:147: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:155: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:164: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:170: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:179: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:183: \item in \describe must have non-empty label
checkRd: (5) metagene.Rd:186: \item in \describe must have non-empty label
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
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
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/metagene.Rcheck/00check.log'
for details.
metagene.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL metagene ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'metagene' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** 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 (metagene)
metagene.Rcheck/tests/runTests.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.
> ## Run all tests in the metagene package
> BiocGenerics:::testPackage("metagene")
Attaching package: 'BiocGenerics'
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, aperm, 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
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data frame : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
Normalization done
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
[1] TRUE
produce data table : ChIP-Seq
produce data table : ChIP-Seq
ChIP-Seq flip/unflip
ChIP-Seq flip/unflip
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
produce data table : ChIP-Seq
[1] TRUE
RUNIT TEST PROTOCOL -- Thu Dec 29 01:16:07 2022
***********************************************
Number of test functions: 204
Number of errors: 0
Number of failures: 0
1 Test Suite :
metagene RUnit Tests - 204 test functions, 0 errors, 0 failures
Number of test functions: 204
Number of errors: 0
Number of failures: 0
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
56.93 2.64 59.53
metagene.Rcheck/metagene-Ex.timings
| name | user | system | elapsed | |
| Bam_Handler | 0.08 | 0.02 | 0.10 | |
| avoid_gaps_update | 0 | 0 | 0 | |
| bed_file_filter | 0 | 0 | 0 | |
| exon_by_gene_with_observed_transcripts | 0 | 0 | 0 | |
| get_demo_bam_files | 0 | 0 | 0 | |
| get_demo_design | 0 | 0 | 0 | |
| get_demo_metagene | 1.33 | 0.06 | 1.39 | |
| get_demo_regions | 0 | 0 | 0 | |
| get_promoters_txdb | 0.00 | 0.02 | 0.02 | |
| metagene | 0.22 | 0.00 | 0.22 | |
| permutation_test | 0 | 0 | 0 | |
| plot_metagene | 0.80 | 0.04 | 0.84 | |
| promoters_hg18 | 0 | 0 | 0 | |
| promoters_hg19 | 0 | 0 | 0 | |
| promoters_mm10 | 0 | 0 | 0 | |
| promoters_mm9 | 0.02 | 0.00 | 0.01 | |
| write_bed_file_filter_result | 0 | 0 | 0 | |