===============================
R CMD BUILD
===============================
* checking for file cypress/DESCRIPTION ... OK
* preparing cypress:
* 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 cypress_0.99.9.tar.gz
===============================
BiocCheckGitClone('cypress')
===============================
BiocCheckVersion: 1.39.26
BiocVersion: 3.19
Package: cypress
PackageVersion: 0.99.9
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3272/1d5554c6a5db07bb0d511a73f3085b5df68f23fd/cypress
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...
* NOTE: (Optional) CITATION file not found. Only include a CITATION
file if there is a preprint or publication for this Bioconductor
package. Note that Bioconductor packages are not required to have
a CITATION file but it is useful both for users and for tracking
Bioconductor project-wide metrics. When including a CITATION
file, add the publication using the 'doi' argument of
'bibentry()'.
BiocCheck results
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3272/1d5554c6a5db07bb0d511a73f3085b5df68f23fd/cypress.Rcheck
* using R Under development (unstable) (2024-03-06 r86056)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file cypress/DESCRIPTION ... OK
* checking extension type ... Package
* this is package cypress version 0.99.9
* 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 cypress 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [9s/9s] OK
* checking loading without being on the library search path ... [9s/9s] 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 ... [35s/35s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) quickPower.Rd:32-33: Lost braces
32 | {IAD: }{whole transcriptome signatures of 6 immune cell subsets. The
| ^
checkRd: (-1) quickPower.Rd:34: Lost braces; missing escapes or markup?
34 | {IBD: }{Inflammatory Bowel Disease}\cr
| ^
checkRd: (-1) quickPower.Rd:34: Lost braces
34 | {IBD: }{Inflammatory Bowel Disease}\cr
| ^
checkRd: (-1) quickPower.Rd:35: Lost braces; missing escapes or markup?
35 | {ASD: }{Autism Spectrum Disorder.}\cr
| ^
checkRd: (-1) quickPower.Rd:35: Lost braces
35 | {ASD: }{Autism Spectrum Disorder.}\cr
| ^
checkRd: (-1) simFromParam.Rd:51-52: Lost braces
51 | {GSE60424: }{whole transcriptome signatures of 6 immune cell subsets.The
| ^
checkRd: (-1) simFromParam.Rd:53: Lost braces; missing escapes or markup?
53 | {IBD: }{Inflammatory Bowel Disease}\cr
| ^
checkRd: (-1) simFromParam.Rd:53: Lost braces
53 | {IBD: }{Inflammatory Bowel Disease}\cr
| ^
checkRd: (-1) simFromParam.Rd:54: Lost braces; missing escapes or markup?
54 | {ASD: }{Autism Spectrum Disorder}\cr
| ^
checkRd: (-1) simFromParam.Rd:54: Lost braces
54 | {ASD: }{Autism Spectrum Disorder}\cr
| ^
* 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 ... [9s/9s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [176s/72s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
simFromParam 115.47 17.957 51.434
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running runTest.R [428s/153s]
[428s/153s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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/3272/1d5554c6a5db07bb0d511a73f3085b5df68f23fd/cypress.Rcheck/00check.log
for details.
===============================
BiocCheck('cypress_0.99.9.tar.gz')
===============================
BiocCheckVersion: 1.39.26
BiocVersion: 3.19
Package: cypress
PackageVersion: 0.99.9
sourceDir: /tmp/RtmpQKp5YU/file28f634703e8142/cypress
installDir: /tmp/RtmpQKp5YU/file28f6341c29f512
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3272/1d5554c6a5db07bb0d511a73f3085b5df68f23fd/cypress.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 recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (33%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* ERROR: Installation calls found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of cypress...
* Checking coding practice...
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 8 functions greater than 50 lines.
* Checking man page documentation...
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* NOTE: Usage of dontrun{} / donttest{} tags found in man page
examples. 7% of man pages use at least one of these tags.
* Checking package NEWS...
* 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; 148 lines (6%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1038 lines
(41%) 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 is in the Support Site Watched Tags.
BiocCheck results
1 ERRORS | 0 WARNINGS | 6 NOTES
See the cypress.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.