===============================
R CMD BUILD
===============================
* checking for file ‘DESpace/DESCRIPTION’ ... OK
* preparing ‘DESpace’:
* 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 ‘DESpace_0.99.8.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/expression plots all cluster_d95bcd3dfb143c84d95ae88f48c4bee0.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/expression plots all cluster_d95bcd3dfb143c84d95ae88f48c4bee0.rdb’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/expression plots all cluster_d95bcd3dfb143c84d95ae88f48c4bee0.rdx’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/expression plots high_low_e2ed34a58998bd04a9cc5bf4b2797221.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_820c6e0309f077f42176671c6a46a4b1.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_820c6e0309f077f42176671c6a46a4b1.rdb’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_820c6e0309f077f42176671c6a46a4b1.rdx’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_f37f7c4d9189f2b6197e2726c27eb8ee.RData’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_f37f7c4d9189f2b6197e2726c27eb8ee.rdb’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_f37f7c4d9189f2b6197e2726c27eb8ee.rdx’
===============================
BiocCheckGitClone('DESpace')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: DESpace
─ PackageVersion: 0.99.8
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/2946/234fa65a1946ace7b4632ac055bb146478c930ed/DESpace
─ 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/2946/234fa65a1946ace7b4632ac055bb146478c930ed/DESpace.Rcheck’
* using R Under development (unstable) (2023-03-16 r83985)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
Apple clang version 12.0.0 (clang-1200.0.32.29)
GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DESpace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DESpace’ version ‘0.99.8’
* 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 ... WARNING
Found the following files with non-portable file names:
vignettes/DESpace_cache/html/DESpace [multi]_ef0a7376549b42f031e02e654e73bf0e.RData
vignettes/DESpace_cache/html/DESpace [multi]_ef0a7376549b42f031e02e654e73bf0e.rdb
vignettes/DESpace_cache/html/DESpace [multi]_ef0a7376549b42f031e02e654e73bf0e.rdx
vignettes/DESpace_cache/html/QC genes_fdc726260c30987002c62e5c2ab3a448.RData
vignettes/DESpace_cache/html/QC genes_fdc726260c30987002c62e5c2ab3a448.rdb
vignettes/DESpace_cache/html/QC genes_fdc726260c30987002c62e5c2ab3a448.rdx
vignettes/DESpace_cache/html/QC spots_496d1c372b7e6b2d2c8d86325f0b172f.RData
vignettes/DESpace_cache/html/QC spots_496d1c372b7e6b2d2c8d86325f0b172f.rdb
vignettes/DESpace_cache/html/QC spots_496d1c372b7e6b2d2c8d86325f0b172f.rdx
vignettes/DESpace_cache/html/expression plots all cluster_d95bcd3dfb143c84d95ae88f48c4bee0.RData
vignettes/DESpace_cache/html/expression plots all cluster_d95bcd3dfb143c84d95ae88f48c4bee0.rdb
vignettes/DESpace_cache/html/expression plots all cluster_d95bcd3dfb143c84d95ae88f48c4bee0.rdx
vignettes/DESpace_cache/html/expression plots high_low_e2ed34a58998bd04a9cc5bf4b2797221.RData
vignettes/DESpace_cache/html/expression plots high_low_e2ed34a58998bd04a9cc5bf4b2797221.rdb
vignettes/DESpace_cache/html/expression plots high_low_e2ed34a58998bd04a9cc5bf4b2797221.rdx
vignettes/DESpace_cache/html/free memory_b55b394a08c786233c71eabfb3cdf711.RData
vignettes/DESpace_cache/html/free memory_b55b394a08c786233c71eabfb3cdf711.rdb
vignettes/DESpace_cache/html/free memory_b55b394a08c786233c71eabfb3cdf711.rdx
vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_820c6e0309f077f42176671c6a46a4b1.RData
vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_820c6e0309f077f42176671c6a46a4b1.rdb
vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_820c6e0309f077f42176671c6a46a4b1.rdx
vignettes/DESpace_cache/html/individual cluster test_b643ea3bc781356e1c95363c1cc24080.RData
vignettes/DESpace_cache/html/individual cluster test_b643ea3bc781356e1c95363c1cc24080.rdb
vignettes/DESpace_cache/html/individual cluster test_b643ea3bc781356e1c95363c1cc24080.rdx
vignettes/DESpace_cache/html/show top results high_fdd993fda19f03d7fef7b0ae2d28ee77.RData
vignettes/DESpace_cache/html/show top results high_fdd993fda19f03d7fef7b0ae2d28ee77.rdb
vignettes/DESpace_cache/html/show top results high_fdd993fda19f03d7fef7b0ae2d28ee77.rdx
vignettes/DESpace_cache/html/show top results low_fd7b46ef84c07278eeafdffd7c832d2c.RData
vignettes/DESpace_cache/html/show top results low_fd7b46ef84c07278eeafdffd7c832d2c.rdb
vignettes/DESpace_cache/html/show top results low_fd7b46ef84c07278eeafdffd7c832d2c.rdx
vignettes/DESpace_cache/html/stLearn[py multi-sample]_e500c9daaee3621be292857ba5370024.RData
vignettes/DESpace_cache/html/stLearn[py multi-sample]_e500c9daaee3621be292857ba5370024.rdb
vignettes/DESpace_cache/html/stLearn[py multi-sample]_e500c9daaee3621be292857ba5370024.rdx
vignettes/DESpace_cache/html/stLearn[r multi-sample]_1d2684286575508682b45663d8d85f21.RData
vignettes/DESpace_cache/html/stLearn[r multi-sample]_1d2684286575508682b45663d8d85f21.rdb
vignettes/DESpace_cache/html/stLearn[r multi-sample]_1d2684286575508682b45663d8d85f21.rdx
vignettes/DESpace_cache/html/top SVGs expression plot [multi]_f37f7c4d9189f2b6197e2726c27eb8ee.RData
vignettes/DESpace_cache/html/top SVGs expression plot [multi]_f37f7c4d9189f2b6197e2726c27eb8ee.rdb
vignettes/DESpace_cache/html/top SVGs expression plot [multi]_f37f7c4d9189f2b6197e2726c27eb8ee.rdx
vignettes/DESpace_cache/html/top SVGs expression plot_b352f118321053ec66fdb9c619b86783.RData
vignettes/DESpace_cache/html/top SVGs expression plot_b352f118321053ec66fdb9c619b86783.rdb
vignettes/DESpace_cache/html/top SVGs expression plot_b352f118321053ec66fdb9c619b86783.rdx
vignettes/DESpace_cache/html/top results WM_dd2c31ce74130d736eee9ded4a43c852.RData
vignettes/DESpace_cache/html/top results WM_dd2c31ce74130d736eee9ded4a43c852.rdb
vignettes/DESpace_cache/html/top results WM_dd2c31ce74130d736eee9ded4a43c852.rdx
vignettes/DESpace_cache/html/top results all_ff004eaab4fbcfc2d68aa5edbb5257fd.RData
vignettes/DESpace_cache/html/top results all_ff004eaab4fbcfc2d68aa5edbb5257fd.rdb
vignettes/DESpace_cache/html/top results all_ff004eaab4fbcfc2d68aa5edbb5257fd.rdx
vignettes/DESpace_cache/html/top results high_low_7b8a94e63682af7a2bd13dfd912c0e5f.RData
vignettes/DESpace_cache/html/top results high_low_7b8a94e63682af7a2bd13dfd912c0e5f.rdb
vignettes/DESpace_cache/html/top results high_low_7b8a94e63682af7a2bd13dfd912c0e5f.rdx
vignettes/DESpace_cache/html/view LIBD layers [multi]_3e66213fb1eac46b5c24680c4cc09e46.RData
vignettes/DESpace_cache/html/view LIBD layers [multi]_3e66213fb1eac46b5c24680c4cc09e46.rdb
vignettes/DESpace_cache/html/view LIBD layers [multi]_3e66213fb1eac46b5c24680c4cc09e46.rdx
vignettes/DESpace_cache/html/view LIBD layers_6d2793293387e50b007947fb20a0406a.RData
vignettes/DESpace_cache/html/view LIBD layers_6d2793293387e50b007947fb20a0406a.rdb
vignettes/DESpace_cache/html/view LIBD layers_6d2793293387e50b007947fb20a0406a.rdx
vignettes/DESpace_cache/html/visualize colData_2c48cf10863db409540942a0ddc8fc12.RData
vignettes/DESpace_cache/html/visualize colData_2c48cf10863db409540942a0ddc8fc12.rdb
vignettes/DESpace_cache/html/visualize colData_2c48cf10863db409540942a0ddc8fc12.rdx
vignettes/DESpace_cache/html/visualize results WM_15d06e8b4a615076c0be18bd0e797d7e.RData
vignettes/DESpace_cache/html/visualize results WM_15d06e8b4a615076c0be18bd0e797d7e.rdb
vignettes/DESpace_cache/html/visualize results WM_15d06e8b4a615076c0be18bd0e797d7e.rdx
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Found the following non-portable file paths:
DESpace/vignettes/DESpace_cache/html/expression plots all cluster_d95bcd3dfb143c84d95ae88f48c4bee0.RData
DESpace/vignettes/DESpace_cache/html/expression plots all cluster_d95bcd3dfb143c84d95ae88f48c4bee0.rdb
DESpace/vignettes/DESpace_cache/html/expression plots all cluster_d95bcd3dfb143c84d95ae88f48c4bee0.rdx
DESpace/vignettes/DESpace_cache/html/expression plots high_low_e2ed34a58998bd04a9cc5bf4b2797221.RData
DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_820c6e0309f077f42176671c6a46a4b1.RData
DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_820c6e0309f077f42176671c6a46a4b1.rdb
DESpace/vignettes/DESpace_cache/html/individual cluster test [multiple-sample]_820c6e0309f077f42176671c6a46a4b1.rdx
DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_f37f7c4d9189f2b6197e2726c27eb8ee.RData
DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_f37f7c4d9189f2b6197e2726c27eb8ee.rdb
DESpace/vignettes/DESpace_cache/html/top SVGs expression plot [multi]_f37f7c4d9189f2b6197e2726c27eb8ee.rdx
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DESpace’ 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 ... [18s/21s] OK
* checking whether the package can be loaded with stated dependencies ... [18s/21s] OK
* checking whether the package can be unloaded cleanly ... [18s/21s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s/20s] OK
* checking whether the namespace can be unloaded cleanly ... [18s/21s] OK
* checking loading without being on the library search path ... [18s/21s] 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 ... [62s/72s] OK
* checking Rd files ... [1s/1s] 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 ... [17s/20s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [59s/69s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DESpace_test 18.249 0.336 21.803
individual_test 6.718 0.182 8.112
top_results 6.793 0.073 8.087
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testhat.R’ [54s/63s]
[54s/63s] 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 ... [9s/11s] OK
* DONE
Status: 1 WARNING
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2946/234fa65a1946ace7b4632ac055bb146478c930ed/DESpace.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('DESpace_0.99.8.tar.gz')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: DESpace
─ PackageVersion: 0.99.8
─ sourceDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpI369VM/file389eb2ed80c/DESpace
─ installDir: /var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpI369VM/file389e7f8cadc4
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/2946/234fa65a1946ace7b4632ac055bb146478c930ed/DESpace.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...
* ERROR: Package tarball exceeds the Bioconductor size requirement.
* Checking individual file sizes...
* WARNING: The following files are over 5MB in size:
'vignettes/DESpace_cache/html/DESpace_bc06cb7dcb8416b32e654a3f0a1760d9.rdb
vignettes/DESpace_cache/html/load-example-data_bcb288d5aee6edbd3073d344ca13f514.rdb
vignettes/DESpace_cache/html/QC
spots_496d1c372b7e6b2d2c8d86325f0b172f.rdb
vignettes/DESpace_cache/html/top SVGs expression plot
[multi]_f37f7c4d9189f2b6197e2726c27eb8ee.rdb
vignettes/DESpace_cache/html/unnamed-chunk-12_42b3aed4e63b49e984e0d0225eff4f2d.rdb
vignettes/DESpace_cache/html/view LIBD layers
[multi]_3e66213fb1eac46b5c24680c4cc09e46.rdb'
* 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 DESpace...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 5 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; 387 lines (15%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 54 lines
(2%) 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 ──
1 ERRORS | 1 WARNINGS | 4 NOTES
See the DESpace.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir DESpace_0.99.8.tar.gz'
>>>>>>>
* installing *source* package ‘DESpace’ ...
** 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 (DESpace)
===============================
R CMD BUILD
===============================
* checking for file ‘DESpace/DESCRIPTION’ ... OK
* preparing ‘DESpace’:
* 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 ‘DESpace_0.99.8.tar.gz’
===============================
BiocCheckGitClone('DESpace')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: DESpace
─ PackageVersion: 0.99.8
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2946/234fa65a1946ace7b4632ac055bb146478c930ed/DESpace
─ 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/2946/234fa65a1946ace7b4632ac055bb146478c930ed/DESpace.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* 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 ‘DESpace/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DESpace’ version ‘0.99.8’
* 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 ‘DESpace’ 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/8s] 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 ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] 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 ... [25s/25s] 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 ... [7s/7s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/26s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DESpace_test 7.709 0.237 7.946
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testhat.R’ [23s/23s]
[23s/23s] 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: OK
===============================
BiocCheck('DESpace_0.99.8.tar.gz')
===============================
─ BiocCheckVersion: 1.35.13
─ BiocVersion: 3.17
─ Package: DESpace
─ PackageVersion: 0.99.8
─ sourceDir: /tmp/RtmpAQbJJx/file30e6e41d27322b/DESpace
─ installDir: /tmp/RtmpAQbJJx/file30e6e43c22c984
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2946/234fa65a1946ace7b4632ac055bb146478c930ed/DESpace.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 DESpace...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 5 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; 387 lines (15%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 54 lines
(2%) 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 | 4 NOTES
See the DESpace.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.