===============================
R CMD BUILD
===============================
* checking for file ‘SurfR/DESCRIPTION’ ... OK
* preparing ‘SurfR’:
* 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 ‘SurfR_0.99.43.tar.gz’
===============================
BiocCheckGitClone('SurfR')
===============================
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.19
─ Package: SurfR
─ PackageVersion: 0.99.43
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3105/cf858f3da9d32009d5e66f7f01b9c13048da92ce/SurfR
─ 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/3105/cf858f3da9d32009d5e66f7f01b9c13048da92ce/SurfR.Rcheck’
* using R Under development (unstable) (2023-11-11 r85510)
* 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 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SurfR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SurfR’ version ‘0.99.43’
* 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 ‘SurfR’ 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] 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 ... [36s/36s] 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [96s/137s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Annotate_SPID 42.756 2.754 60.092
TCGA_download 9.551 0.066 11.748
Gene2SProtein 8.452 0.132 8.585
DownloadArchS4 0.964 0.038 14.521
enrichr_download 0.092 0.004 7.700
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [44s/58s]
[44s/58s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
final dispersion estimates
fitting model and testing
[ FAIL 1 | WARN 1 | SKIP 1 | PASS 18 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_SurfR.R:126:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_SurfR.R:88:3'): Annotate_SPID ────────────────────────────────
Expected `Annotate_SPID(ind_deg$DEG2_df, "WikiPathway_2023_Human")` to run without any errors.
i Actually got a <simpleError> with text:
argument is of length zero
[ FAIL 1 | WARN 1 | SKIP 1 | PASS 18 ]
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 ... [3s/3s] OK
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3105/cf858f3da9d32009d5e66f7f01b9c13048da92ce/SurfR.Rcheck/00check.log’
for details.
===============================
BiocCheck('SurfR_0.99.43.tar.gz')
===============================
─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.19
─ Package: SurfR
─ PackageVersion: 0.99.43
─ sourceDir: /tmp/Rtmpb5DzpJ/file376b56529ee30b/SurfR
─ installDir: /tmp/Rtmpb5DzpJ/file376b565848b41f
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3105/cf858f3da9d32009d5e66f7f01b9c13048da92ce/SurfR.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 4.3.0 to 4.4.0.
* 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...
* 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 recommeded fields in DESCRIPTION...
* 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 SurfR...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 11 functions greater than 50 lines.
* Checking man page documentation...
* 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; 262 lines (8%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 746 lines
(24%) 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 | 6 NOTES
See the SurfR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.