| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:45 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 TimiRGeN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TimiRGeN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 2069/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TimiRGeN 1.11.0 (landing page) Krutik Patel
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: TimiRGeN |
| Version: 1.11.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:TimiRGeN.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings TimiRGeN_1.11.0.tar.gz |
| StartedAt: 2023-05-30 21:24:49 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 21:35:14 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 624.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TimiRGeN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:TimiRGeN.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings TimiRGeN_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/TimiRGeN.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘TimiRGeN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TimiRGeN’ version ‘1.11.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TimiRGeN’ 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 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 ... OK
* 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 ... NOTE
Note: found 3 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
wikiMrna 5.104 0.168 12.122
clusterList 4.464 0.232 7.122
quickTCPred 4.220 0.168 6.681
quickReg 4.143 0.152 7.106
addIds 3.999 0.260 12.200
quickPathwayTC 3.950 0.164 7.198
dloadGmt 3.971 0.124 10.435
quickDMap 3.912 0.083 8.167
quickTC 3.885 0.099 6.139
linearRegr 3.693 0.195 6.050
quickHClust 3.753 0.104 7.039
multiReg 3.661 0.184 7.336
quickDendro 3.684 0.127 7.739
makeDynamic 3.550 0.140 9.021
quickCrossCorr 3.494 0.144 5.987
eNames 3.106 0.172 5.414
diffExpressRes 3.117 0.116 5.897
makeMapp 2.920 0.099 5.840
quickBar 2.838 0.068 6.687
enrichWiki 2.713 0.125 6.546
gmtEnsembl 1.996 0.037 6.073
* 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 ...
‘TimiRGeN_tutorial.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.18-bioc/meat/TimiRGeN.Rcheck/00check.log’
for details.
TimiRGeN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL TimiRGeN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘TimiRGeN’ ... ** 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 (TimiRGeN)
TimiRGeN.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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.
> #unit test check
> library(testthat)
> library(TimiRGeN)
Loading required package: Mfuzz
Loading required package: Biobase
Loading required package: BiocGenerics
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
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: e1071
Attaching package: 'DynDoc'
The following object is masked from 'package:BiocGenerics':
path
Loading required package: MultiAssayExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
The following object is masked from 'package:Biobase':
rowMedians
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Loading required package: GenomeInfoDb
> test_check(package = "TimiRGeN")
[ FAIL 0 | WARN 49 | SKIP 0 | PASS 124 ]
[ FAIL 0 | WARN 49 | SKIP 0 | PASS 124 ]
>
> proc.time()
user system elapsed
29.375 1.922 31.283
TimiRGeN.Rcheck/TimiRGeN-Ex.timings
| name | user | system | elapsed | |
| UUO_data | 0.003 | 0.004 | 0.007 | |
| addIds | 3.999 | 0.260 | 12.200 | |
| addPrefix | 0.638 | 0.012 | 0.650 | |
| clusterCheck | 1.091 | 0.057 | 4.234 | |
| clusterList | 4.464 | 0.232 | 7.122 | |
| combineGenes | 0.381 | 0.016 | 0.397 | |
| createClusters | 0.944 | 0.024 | 3.949 | |
| createClusters2 | 0.752 | 0.024 | 0.776 | |
| cytoMake | 0 | 0 | 0 | |
| diffExpressRes | 3.117 | 0.116 | 5.897 | |
| dloadGmt | 3.971 | 0.124 | 10.435 | |
| dloadMirdb | 0 | 0 | 0 | |
| dloadMirtarbase | 0.294 | 0.008 | 0.302 | |
| dloadTargetscan | 0.000 | 0.000 | 0.001 | |
| eNames | 3.106 | 0.172 | 5.414 | |
| e_list_mouse | 0.002 | 0.000 | 0.002 | |
| enrichWiki | 2.713 | 0.125 | 6.546 | |
| genesList | 0.783 | 0.020 | 0.804 | |
| getIdsMir | 0.875 | 0.032 | 0.906 | |
| getIdsMrna | 2.000 | 0.084 | 4.608 | |
| gmtEnsembl | 1.996 | 0.037 | 6.073 | |
| hs_mRNA | 0.002 | 0.000 | 0.001 | |
| hs_miR | 0.001 | 0.000 | 0.002 | |
| hs_probes | 0.001 | 0.000 | 0.002 | |
| linearRegr | 3.693 | 0.195 | 6.050 | |
| long_data | 0.004 | 0.000 | 0.003 | |
| makeDynamic | 3.550 | 0.140 | 9.021 | |
| makeMapp | 2.920 | 0.099 | 5.840 | |
| makeNet | 0.064 | 0.008 | 0.072 | |
| matrixFilter | 0.304 | 0.004 | 0.308 | |
| miRTarBase | 0.001 | 0.000 | 0.002 | |
| mirMrnaInt | 0.277 | 0.008 | 0.285 | |
| mm_mRNA | 0.000 | 0.002 | 0.002 | |
| mm_miR | 0.000 | 0.001 | 0.002 | |
| multiReg | 3.661 | 0.184 | 7.336 | |
| quickBar | 2.838 | 0.068 | 6.687 | |
| quickCrossCorr | 3.494 | 0.144 | 5.987 | |
| quickDMap | 3.912 | 0.083 | 8.167 | |
| quickDendro | 3.684 | 0.127 | 7.739 | |
| quickFuzz | 0.949 | 0.020 | 3.938 | |
| quickHClust | 3.753 | 0.104 | 7.039 | |
| quickMap | 0.356 | 0.004 | 0.360 | |
| quickNet | 0.149 | 0.000 | 0.149 | |
| quickPathwayTC | 3.950 | 0.164 | 7.198 | |
| quickReg | 4.143 | 0.152 | 7.106 | |
| quickTC | 3.885 | 0.099 | 6.139 | |
| quickTCPred | 4.220 | 0.168 | 6.681 | |
| reduceWiki | 0.400 | 0.012 | 0.412 | |
| returnCluster | 1.203 | 0.056 | 4.317 | |
| significantVals | 0.368 | 0.012 | 0.380 | |
| startObject | 0.146 | 0.000 | 0.145 | |
| turnPercent | 0.545 | 0.012 | 0.557 | |
| w_list_mouse | 0.002 | 0.000 | 0.002 | |
| wikiMatrix | 0.272 | 0.012 | 0.284 | |
| wikiMrna | 5.104 | 0.168 | 12.122 | |