===============================
R CMD BUILD
===============================
* checking for file ‘Rcollectl/DESCRIPTION’ ... OK
* preparing ‘Rcollectl’:
* 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
* building ‘Rcollectl_0.99.3.tar.gz’
===============================
BiocCheckGitClone('Rcollectl')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: Rcollectl
─ PackageVersion: 0.99.3
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2948/5339d99fdcb7bb9a7a482a049b25c7b6019f49ec/Rcollectl
─ 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/2948/5339d99fdcb7bb9a7a482a049b25c7b6019f49ec/Rcollectl.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-pc-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
* using option ‘--no-vignettes’
* checking for file ‘Rcollectl/DESCRIPTION’ ... OK
* this is package ‘Rcollectl’ version ‘0.99.3’
* 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:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘Rcollectl’ 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... OK
* checking R code for possible problems ... [4s/4s] NOTE
plot_usage: no visible binding for global variable ‘tm’
plot_usage: no visible binding for global variable ‘value’
plot_usage: no visible binding for global variable ‘type’
Undefined global functions or variables:
tm type value
* 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 files in ‘vignettes’ ... OK
* checking examples ... [4s/32s] ERROR
Running examples in ‘Rcollectl-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cl_timestamp
> ### Title: Functions to add time stamps to collectl output
> ### Aliases: cl_timestamp cl_timestamp_layer cl_timestamp_label
>
> ### ** Examples
>
> id <- cl_start()
> Sys.sleep(2)
> #code
> cl_timestamp(id, "step1")
> Sys.sleep(2)
> # code
> Sys.sleep(2)
> cl_timestamp(id, "step2")
> Sys.sleep(2)
> # code
> Sys.sleep(2)
> cl_timestamp(id, "step3")
> Sys.sleep(2)
> # code
> cl_stop(id)
> path <- cl_result_path(id)
>
> plot_usage(cl_parse(path)) +
+ cl_timestamp_layer(path) +
+ cl_timestamp_label(path) +
+ ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust=1))
Error in read.table(file = file, header = header, sep = sep, quote = quote, :
more columns than column names
Calls: plot_usage ... data.frame -> as.POSIXct -> cl_parse -> read.delim -> read.table
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [5s/12s]
[5s/12s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(Rcollectl)
>
> test_check("Rcollectl")
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 7 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('tests.R:36'): it works ──────────────────────────────────────────────
Error in `read.table(file = file, header = header, sep = sep, quote = quote,
dec = dec, fill = fill, comment.char = comment.char, ...)`: more columns than column names
Backtrace:
▆
1. └─Rcollectl::cl_parse(targ) at tests.R:36:2
2. └─utils::read.delim(...)
3. └─utils::read.table(...)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 7 ]
Error: Test failures
Execution halted
* 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 ... [2s/2s] OK
* DONE
Status: 2 ERRORs, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2948/5339d99fdcb7bb9a7a482a049b25c7b6019f49ec/Rcollectl.Rcheck/00check.log’
for details.
===============================
BiocCheck('Rcollectl_0.99.3.tar.gz')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: Rcollectl
─ PackageVersion: 0.99.3
─ sourceDir: /tmp/RtmpC4IlvR/file2c54f361150281/Rcollectl
─ installDir: /tmp/RtmpC4IlvR/file2c54f35df2c405
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2948/5339d99fdcb7bb9a7a482a049b25c7b6019f49ec/Rcollectl.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...
* 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...
* 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 Rcollectl...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
* 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; 19 lines (3%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 6 lines (1%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 99 lines
(14%) 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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 5 NOTES
See the Rcollectl.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.