Nicolas Servant
| Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/HiTC |
| git_branch: RELEASE_3_17 |
| git_last_commit: 32e63b6 |
| git_last_commit_date: 2023-04-25 10:22:49 -0400 (Tue, 25 Apr 2023) |
| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-10-16 11:35:26 -0400 (Mon, 16 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4626 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4379 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4395 |
| 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 | ||||
| Package 942/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HiTC 1.44.0 (landing page) Nicolas Servant
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the HiTC package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiTC.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: HiTC |
| Version: 1.44.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HiTC_1.44.0.tar.gz |
| StartedAt: 2023-10-15 22:02:07 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 22:08:41 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 394.2 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: HiTC.Rcheck |
| Warnings: 2 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:HiTC.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings HiTC_1.44.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/HiTC.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘HiTC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiTC’ version ‘1.44.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘HiTC’ 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 ... NOTE
Problems with news in ‘NEWS’:
Cannot process chunk/lines:
SIGNIFICANT USER-VISIBLE CHANGES
Cannot process chunk/lines:
BUG FIXES
Cannot process chunk/lines:
NEW FEATURES
* 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 ... NOTE
directionalityIndex: no visible global function definition for
‘subjectHits’
directionalityIndex: no visible global function definition for
‘queryHits’
getBlocsIndex: no visible global function definition for ‘Rle’
getExpectedCountsMean: no visible global function definition for ‘Rle’
normLGF: no visible global function definition for ‘glm.nb’
slidingWindow: no visible binding for global variable ‘consV’
splitCombinedContacts : <anonymous>: no visible global function
definition for ‘seqlevels<-’
divide,HTCexp-HTCexp: no visible global function definition for
‘queryHits’
divide,HTCexp-HTCexp: no visible global function definition for
‘subjectHits’
isBinned,HTCexp: no visible global function definition for
‘countMatches’
substract,HTCexp-HTCexp: no visible global function definition for
‘queryHits’
substract,HTCexp-HTCexp: no visible global function definition for
‘subjectHits’
Undefined global functions or variables:
Rle consV countMatches glm.nb queryHits seqlevels<- subjectHits
* checking Rd files ... WARNING
checkRd: (5) HTClist-class.Rd:52-54: \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 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
directionalityIndex 16.835 0.536 17.373
CQC 5.147 0.128 5.276
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘HiC_analysis.Rnw’... failed
‘HiTC.Rnw’... OK
WARNING
Errors in running code in vignettes:
when running code in ‘HiC_analysis.Rnw’
...
> resFrag <- getRestrictionFragmentsPerChromosome(resSite = "AAGCTT",
+ overhangs5 = 1, chromosomes = "chr6", genomePack = "BSgenome.Hsapiens.UCS ..." ... [TRUNCATED]
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘BSgenome.Hsapiens.UCSC.hg18’
When sourcing ‘HiC_analysis.R’:
Error: require(genomePack, character.only = TRUE) is not TRUE
Execution halted
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘HiC_analysis.Rnw’ using Sweave
Loading required package: HiTC
Loading required package: IRanges
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
Loading required package: S4Vectors
Loading required package: stats4
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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: HiCDataHumanIMR90
'as(<dsCMatrix>, "dgTMatrix")' is deprecated.
Use 'as(as(., "generalMatrix"), "TsparseMatrix")' instead.
See help("Deprecated") and help("Matrix-deprecated").
Warning: file stem ‘./HiTC-plot1’ is not portable
Bin size 'xgi' =5e+05 [1x5e+05]
Bin size 'ygi' =5e+05 [1x5e+05]
Bin size 'xgi' =5e+05 [1x5e+05]
Bin size 'ygi' =5e+05 [1x5e+05]
Bin size 'xgi' =5e+05 [1x5e+05]
Bin size 'ygi' =5e+05 [1x5e+05]
Bin size 'xgi' =5e+05 [1x5e+05]
Bin size 'ygi' =5e+05 [1x5e+05]
Bin size 'xgi' =5e+05 [1x5e+05]
Bin size 'ygi' =5e+05 [1x5e+05]
Bin size 'xgi' =5e+05 [1x5e+05]
Bin size 'ygi' =5e+05 [1x5e+05]
Plotting chr5chr5...
minrange= 2 - maxrange= 569
Plotting chr5chr6...
minrange= 1 - maxrange= 8
Plotting chr5chr7...
minrange= 1 - maxrange= 8
Plotting chr6chr6...
minrange= 3 - maxrange= 593.02
Plotting chr6chr7...
minrange= 1 - maxrange= 8
Plotting chr7chr7...
minrange= 2 - maxrange= 571
Warning: file stem ‘./HiTC-plot2’ is not portable
Plotting chr5chr5...
minrange= 1 - maxrange= 200
Plotting chr5chr6...
minrange= 1 - maxrange= 200
Plotting chr5chr7...
minrange= 1 - maxrange= 119
Plotting chr6chr5...
minrange= 1 - maxrange= 200
Plotting chr6chr6...
minrange= 1 - maxrange= 200
Plotting chr6chr7...
minrange= 1 - maxrange= 81
Plotting chr7chr5...
minrange= 1 - maxrange= 119
Plotting chr7chr6...
minrange= 1 - maxrange= 81
Plotting chr7chr7...
minrange= 1 - maxrange= 200
Loading required package: BSgenome.Hsapiens.UCSC.hg18
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘BSgenome.Hsapiens.UCSC.hg18’
Error: processing vignette 'HiC_analysis.Rnw' failed with diagnostics:
chunk 6 (label = resFrag)
Error in getRestrictionFragmentsPerChromosome(resSite = "AAGCTT", overhangs5 = 1, :
require(genomePack, character.only = TRUE) is not TRUE
--- failed re-building ‘HiC_analysis.Rnw’
--- re-building ‘HiTC.Rnw’ using Sweave
Loading required package: IRanges
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
Loading required package: S4Vectors
Loading required package: stats4
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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:S4Vectors’:
expand
Reading file ...
Convert my5C matrix file in HTCexp object(s)
Reading file ...
Convert my5C matrix file in HTCexp object(s)
Reading file ...
Convert my5C matrix file in HTCexp object(s)
Reading file ...
Convert my5C matrix file in HTCexp object(s)
Reading file ...
Convert my5C matrix file in HTCexp object(s)
Reading file ...
Convert my5C matrix file in HTCexp object(s)
'as(<dsCMatrix>, "dgTMatrix")' is deprecated.
Use 'as(as(., "generalMatrix"), "TsparseMatrix")' instead.
See help("Deprecated") and help("Matrix-deprecated").
Warning: file stem ‘./HiTC-qcc’ is not portable
Get data ...
Generate quality control plots ...
minrange= 1 - maxrange= 741
Warning: file stem ‘./HiTC-bin5C’ is not portable
Bin size 'xgi' =102420 [3x34140]
Bin size 'ygi' =102420 [3x34140]
minrange= 3 - maxrange= 477.2
Lowess fit ...
Standard deviation calculation ...
Delta=8876.395
Calculating stdev ...
Warning: file stem ‘./HiTC-norm5Cznorm’ is not portable
Lowess fit ...
Standard deviation calculation ...
Delta=8876.395
Calculating stdev ...
minrange= 0.027 - maxrange= 2.139
Warning: file stem ‘./HiTC-annot5C’ is not portable
Bin size 'xgi' =102087 [3x34029]
Bin size 'ygi' =102087 [3x34029]
Loading required package: rtracklayer
minrange= 0.5 - maxrange= 10
Warning: file stem ‘./HiTC-comp5C’ is not portable
Bin size 'xgi' =102087 [3x34029]
Bin size 'ygi' =102087 [3x34029]
minrange= 0.5 - maxrange= 10
minrange= 0.5 - maxrange= 10
Warning: file stem ‘./HiTC-mapClist’ is not portable
Plotting chr12chr12...
minrange= 1 - maxrange= 100
Plotting chr12chr13...
minrange= 1 - maxrange= 20
Plotting chr12chr14...
minrange= 1 - maxrange= 39
Plotting chr13chr13...
minrange= 1 - maxrange= 100
Plotting chr13chr14...
minrange= 1 - maxrange= 18
Plotting chr14chr14...
minrange= 1 - maxrange= 100
Warning: file stem ‘./HiTC-mapChic’ is not portable
Plotting chr14chr14...
minrange= 1 - maxrange= 100
Warning: file stem ‘./HiTC-mapNormhic’ is not portable
Lowess fit ...
Plotting chr14chr14...
minrange= 0.015 - maxrange= 2.519
Warning: file stem ‘./HiTC-mapCorhic’ is not portable
Plotting chr14chr14...
minrange= 0 - maxrange= 1
Warning: file stem ‘./HiTC-mapPCAhic’ is not portable
Lowess fit ...
--- finished re-building ‘HiTC.Rnw’
SUMMARY: processing the following file failed:
‘HiC_analysis.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/HiTC.Rcheck/00check.log’
for details.
HiTC.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL HiTC ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘HiTC’ ... ** using staged installation ** R ** data ** 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 (HiTC)
HiTC.Rcheck/HiTC-Ex.timings
| name | user | system | elapsed | |
| CQC | 5.147 | 0.128 | 5.276 | |
| HTCexp-class | 3.363 | 0.164 | 3.526 | |
| HTClist-class | 1.114 | 0.012 | 1.128 | |
| Nora_5C | 0.195 | 0.000 | 0.196 | |
| binningC | 0.973 | 0.004 | 0.977 | |
| directionalityIndex | 16.835 | 0.536 | 17.373 | |
| discretize | 0 | 0 | 0 | |
| export.my5C | 0 | 0 | 0 | |
| exportC | 0 | 0 | 0 | |
| extractRegion | 0.349 | 0.000 | 0.349 | |
| getAnnotatedRestrictionSites | 0.000 | 0.000 | 0.001 | |
| getExpectedCounts | 1.694 | 0.387 | 1.967 | |
| getPearsonMap | 0.453 | 0.036 | 0.489 | |
| getRestrictionFragmentsPerChromosome | 0 | 0 | 0 | |
| import.my5C | 0.097 | 0.012 | 0.109 | |
| importC | 0.001 | 0.000 | 0.001 | |
| intervalsDist | 0.373 | 0.000 | 0.373 | |
| mapC | 3.364 | 0.024 | 3.388 | |
| normICE | 0 | 0 | 0 | |
| normLGF | 0.001 | 0.000 | 0.001 | |
| pca.hic | 0.419 | 0.004 | 0.423 | |
| removeIntervals | 0.232 | 0.000 | 0.232 | |
| setGenomicFeatures | 0 | 0 | 0 | |
| setIntervalScale | 0.815 | 0.008 | 0.823 | |