| Back to Build/check report for BioC 3.17 |
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This page was generated on 2023-01-02 09:00:31 -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 GenomicScores package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 779/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GenomicScores 2.11.0 (landing page) Robert Castelo
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ||||||||
| Package: GenomicScores |
| Version: 2.11.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GenomicScores.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomicScores_2.11.0.tar.gz |
| StartedAt: 2022-12-29 00:06:15 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 00:10:08 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 233.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: GenomicScores.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:GenomicScores.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings GenomicScores_2.11.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/GenomicScores.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 'GenomicScores/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GenomicScores' version '2.11.0'
* 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 ... NOTE
Found the following hidden files and directories:
inst/gscores-template/inst/extdata/.gitkeep
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'GenomicScores' 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
* 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
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
'hdf5Backend'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
checkRd: (5) GScores-class.Rd:129-160: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:166-168: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:169-174: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:175-177: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:178-180: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:181-183: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:184-186: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:187-189: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:190-192: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:193-195: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:196-200: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:201-203: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:204-206: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:207-209: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:210-213: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:214-217: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:218-220: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:221-223: \item in \describe must have non-empty label
checkRd: (5) GScores-class.Rd:224-227: \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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
GScores-class 10.61 0.45 14.92
gscores 8.07 0.81 11.91
availableGScores 3.77 2.08 28.61
* 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/GenomicScores.Rcheck/00check.log'
for details.
GenomicScores.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL GenomicScores ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library' * installing *source* package 'GenomicScores' ... ** using staged installation ** R ** 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 (GenomicScores)
GenomicScores.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.
> BiocGenerics:::testPackage("GenomicScores")
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
Attaching package: 'GenomicScores'
The following object is masked from 'package:utils':
citation
Loading required package: phastCons100way.UCSC.hg19
RUNIT TEST PROTOCOL -- Thu Dec 29 00:09:57 2022
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
GenomicScores RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
14.31 0.96 16.96
GenomicScores.Rcheck/GenomicScores-Ex.timings
| name | user | system | elapsed | |
| GScores-class | 10.61 | 0.45 | 14.92 | |
| availableGScores | 3.77 | 2.08 | 28.61 | |
| gscores | 8.07 | 0.81 | 11.91 | |
| igscores | 0 | 0 | 0 | |
| makeGScoresPackage | 0 | 0 | 0 | |
| rgscores | 2.33 | 0.25 | 2.59 | |
| wgscores | 1.47 | 0.18 | 2.38 | |