nebbiolo1 Summary
[top]
| Package: HiCExperiment |
| Version: 0.99.0 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiCExperiment |
| BuildTime: 2 minutes 12.58 seconds |
| CheckCommand: BiocCheckGitClone('HiCExperiment') && /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/2879/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/2879/HiCExperiment_20230103193832/HiCExperiment.install-out.txt HiCExperiment_0.99.0.tar.gz && BiocCheck('HiCExperiment_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 10 minutes 56.18 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 993.16 KiB |
| BuildID:: HiCExperiment_20230103193832 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: HiCExperiment. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘HiCExperiment/DESCRIPTION’ ... OK
* preparing ‘HiCExperiment’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘HiCExperiment_0.99.0.tar.gz’
nebbiolo1 CHECK output
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===============================
BiocCheckGitClone('HiCExperiment')
===============================
─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: HiCExperiment
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2879/HiCExperiment_20230103193832/HiCExperiment
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2879/HiCExperiment_20230103193832/HiCExperiment.Rcheck’
* using R Under development (unstable) (2022-12-10 r83428)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCExperiment/DESCRIPTION’ ... OK
* this is package ‘HiCExperiment’ version ‘0.99.0’
* 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 ‘HiCExperiment’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call("_H5Fis_hdf5", ..., PACKAGE = "rhdf5")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [27s/27s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [2s/2s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [123s/128s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
data 21.627 3.987 28.915
import-methods 17.912 1.715 15.371
AggrHiCExperiment 14.582 1.947 16.570
parse-other 11.689 2.491 14.448
HiCExperiment-methods 5.716 0.789 7.060
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [394s/377s]
[394s/377s] 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 ... [3s/3s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2879/HiCExperiment_20230103193832/HiCExperiment.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('HiCExperiment_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: HiCExperiment
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/RtmpoiYtR2/file1eb7ff1e32c9f5/HiCExperiment
─ installDir: /tmp/RtmpoiYtR2/file1eb7ff70050362
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2879/HiCExperiment_20230103193832/HiCExperiment.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of HiCExperiment...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 143 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Add non-empty \value sections to the following man
pages:
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 178 lines (4%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 60 lines
(1%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
* NOTE: Cannot determine whether maintainer is subscribed to the
Bioc-Devel mailing list (requires admin credentials). Subscribe
here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
─ BiocCheck results ──
1 ERRORS | 1 WARNINGS | 12 NOTES
See the HiCExperiment.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo1 BUILD BIN output
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merida1 Summary
[top]
| Package: HiCExperiment |
| Version: 0.99.0 |
| RVersion: 4.3
|
| BiocVersion: 3.17
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data HiCExperiment |
| BuildTime: 2 minutes 19.24 seconds |
| CheckCommand: BiocCheckGitClone('HiCExperiment') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/2879/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/2879/HiCExperiment_20230103193832/HiCExperiment.install-out.txt HiCExperiment_0.99.0.tar.gz && BiocCheck('HiCExperiment_0.99.0.tar.gz', `new-package`=TRUE) |
| CheckTime: 10 minutes 19.69 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh HiCExperiment_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 27.66 seconds |
| PackageFileSize: 993.04 KiB |
| BuildID:: HiCExperiment_20230103193832 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: HiCExperiment. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘HiCExperiment/DESCRIPTION’ ... OK
* preparing ‘HiCExperiment’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘HiCExperiment_0.99.0.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('HiCExperiment')
===============================
─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: HiCExperiment
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2879/HiCExperiment_20230103193832/HiCExperiment
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2879/HiCExperiment_20230103193832/HiCExperiment.Rcheck’
* using R Under development (unstable) (2022-12-10 r83428)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCExperiment/DESCRIPTION’ ... OK
* this is package ‘HiCExperiment’ version ‘0.99.0’
* 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 ‘HiCExperiment’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
.Call("_H5Fis_hdf5", ..., PACKAGE = "rhdf5")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... [32s/32s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [3s/3s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [67s/72s] ERROR
Running examples in ‘HiCExperiment-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: data
> ### Title: Example datasets provided in 'HiCExperiment' & 'HiContactsData'
> ### Aliases: data centros_yeast contacts_yeast contacts_yeast_eco1
> ### full_contacts_yeast
>
> ### ** Examples
>
> data(centros_yeast)
> centros_yeast
GRanges object with 16 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] I 151583-151641 +
[2] II 238361-238419 +
[3] III 114322-114380 +
[4] IV 449879-449937 +
[5] V 152522-152580 +
... ... ... ...
[12] XII 151366-151424 +
[13] XIII 268222-268280 +
[14] XIV 628588-628646 +
[15] XV 326897-326955 +
[16] XVI 556255-556313 +
-------
seqinfo: 17 sequences (1 circular) from R64-1-1 genome
> contacts_yeast()
snapshotDate(): 2022-12-16
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
loading from cache
`HiCExperiment` object with 2,945,692 interactions over 11,676 regions
-------
fileName: "/Users/pkgbuild/Library/Caches/org.R-project.R/R/ExperimentHub/d369332250d6_7752"
focus: "whole genome"
resolutions(5): 1000 2000 4000 8000 16000
current resolution: 1000
interactions: 2945692
scores(2): count balanced
topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0)
pairsFile: N/A
metadata(0):
> contacts_yeast_eco1()
snapshotDate(): 2022-12-16
see ?HiContactsData and browseVignettes('HiContactsData') for documentation
downloading 1 resources
retrieving 1 resource
Warning: download failed
web resource path: ‘https://experimenthub.bioconductor.org/fetch/7754’
local file path: ‘/Users/pkgbuild/Library/Caches/org.R-project.R/R/ExperimentHub/d52178e0c2dd_7754’
reason: Internal Server Error (HTTP 500).
Warning: bfcadd() failed; resource removed
rid: BFC144
fpath: ‘https://experimenthub.bioconductor.org/fetch/7754’
reason: download failed
Warning: download failed
hub path: ‘https://experimenthub.bioconductor.org/fetch/7754’
cache resource: ‘EH7704 : 7754’
reason: bfcadd() failed; see warnings()
Error: failed to load resource
name: EH7704
title: Eco1-AID yeast Hi-C mcool
reason: 1 resources failed to download
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [380s/379s]
[380s/379s] 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 ... [5s/5s] OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2879/HiCExperiment_20230103193832/HiCExperiment.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('HiCExperiment_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.35.8
─ BiocVersion: 3.17
─ Package: HiCExperiment
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpJdWfmg/filed78525b3fae9/HiCExperiment
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpJdWfmg/filed785190398fa
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2879/HiCExperiment_20230103193832/HiCExperiment.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of HiCExperiment...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid the use of 'paste' in condition signals
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 143 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Add non-empty \value sections to the following man
pages:
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 178 lines (4%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 60 lines
(1%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
* NOTE: Cannot determine whether maintainer is subscribed to the
Bioc-Devel mailing list (requires admin credentials). Subscribe
here: https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
Maintainer is registered at support site.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
─ BiocCheck results ──
1 ERRORS | 1 WARNINGS | 12 NOTES
See the HiCExperiment.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
merida1 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir HiCExperiment_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘HiCExperiment’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (HiCExperiment)