nebbiolo2 Summary
[top]
| Package: compSPOT |
| Version: 0.99.10 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data compSPOT |
| BuildTime: 0 minutes 27.83 seconds |
| CheckCommand: BiocCheckGitClone('compSPOT') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3079/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3079/ab0e0df39d69e5ff3b6dfad92c38e94e1ad0a321/compSPOT.install-out.txt compSPOT_0.99.10.tar.gz && BiocCheck('compSPOT_0.99.10.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 20.51 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 2004.91 KiB |
| BuildID:: compSPOT_20230828192836 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: compSPOT. 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. Adding Build Product Information to Database.Checking Package status: 1. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘compSPOT/DESCRIPTION’ ... OK
* preparing ‘compSPOT’:
* 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 ‘compSPOT_0.99.10.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('compSPOT')
===============================
─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: compSPOT
─ PackageVersion: 0.99.10
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3079/ab0e0df39d69e5ff3b6dfad92c38e94e1ad0a321/compSPOT
─ 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/3079/ab0e0df39d69e5ff3b6dfad92c38e94e1ad0a321/compSPOT.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compSPOT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compSPOT’ version ‘0.99.10’
* 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 ‘compSPOT’ 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 ... WARNING
Dependence on R version ‘4.3.1’ not with patchlevel 0
* 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 ... [5s/5s] NOTE
compare_features : count_mutations: no visible binding for global
variable ‘Sample’
compare_features : count_mutations: no visible binding for global
variable ‘Chromosome’
count_groups: no visible binding for global variable ‘Group’
count_mutations: no visible binding for global variable ‘Sample’
count_mutations: no visible binding for global variable ‘Chromosome’
find_hotspots: no visible binding for global variable ‘percent’
plot_ecdf: no visible binding for global variable ‘Hotspot’
plot_ecdf: no visible binding for global variable ‘Mutation_Count’
plot_ecdf: no visible binding for global variable ‘Group’
plot_features: no visible global function definition for ‘na.omit’
plot_features: no visible binding for global variable ‘Count’
plot_sigspot: no visible binding for global variable ‘percent’
plot_sigspot: no visible binding for global variable ‘number’
plot_sigspot: no visible binding for global variable ‘Label’
plot_sigspot: no visible binding for global variable ‘type’
plot_sigspot: no visible binding for global variable ‘Count’
plot_sigspot: no visible binding for global variable ‘Group’
plot_spot: no visible binding for global variable ‘Mutation_Count’
plot_spot: no visible binding for global variable ‘Hotspot’
plot_spot: no visible binding for global variable ‘Group’
region_counter: no visible binding for global variable ‘Sample’
region_counter: no visible binding for global variable ‘Chromosome’
spot_rank: no visible binding for global variable ‘Chromosome’
Undefined global functions or variables:
Chromosome Count Group Hotspot Label Mutation_Count Sample na.omit
number percent type
Consider adding
importFrom("stats", "na.omit")
to your NAMESPACE file.
* 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 ... [140s/95s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
compare_groups 125.434 1.251 81.428
find_hotspots 8.123 0.072 8.195
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [10s/10s]
[11s/11s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
1. └─base::lapply(...) at test-check_features.R:4:0
2. └─compSPOT (local) FUN(X[[i]], ...)
3. └─stats::na.omit(df)
── Error ('test-check_groups.R:12:1'): (code run outside of `test_that()`) ─────
Error in `eval(code, test_env)`: object 'regions' not found
Backtrace:
▆
1. ├─data.table::rbindlist(lapply(seq_len(nrow(regions)), count_groups)) at test-check_groups.R:12:0
2. ├─base::lapply(seq_len(nrow(regions)), count_groups)
3. └─base::nrow(regions)
── Error ('test-check_ranking.R:17:1'): (code run outside of `test_that()`) ────
Error in `seq_len(nrow(ranked_regions))[[-length(seq_len(nrow(ranked_regions)))]]`: attempt to select more than one element in integerOneIndex
Backtrace:
▆
1. └─base::lapply(...) at test-check_ranking.R:17:0
── Error ('test-spots.R:6:1'): (code run outside of `test_that()`) ─────────────
Error in `sig.spots(data = example_mutations, regions = example_regions,
pvalue = pval, threshold = thres, include_genes = TRUE, rank = TRUE)`: could not find function "sig.spots"
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ]
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: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3079/ab0e0df39d69e5ff3b6dfad92c38e94e1ad0a321/compSPOT.Rcheck/00check.log’
for details.
===============================
BiocCheck('compSPOT_0.99.10.tar.gz')
===============================
─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: compSPOT
─ PackageVersion: 0.99.10
─ sourceDir: /tmp/RtmpLX1uAv/fileb1c6d73fa5018/compSPOT
─ installDir: /tmp/RtmpLX1uAv/fileb1c6d76211220
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3079/ab0e0df39d69e5ff3b6dfad92c38e94e1ad0a321/compSPOT.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...
* WARNING: Package files exceed the 5MB size limit.
* 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 compSPOT...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 6 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; 11 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 360 lines
(19%) 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 | 1 WARNINGS | 3 NOTES
See the compSPOT.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]
lconway Summary
[top]
| Package: compSPOT |
| Version: 0.99.10 |
| RVersion: 4.3
|
| BiocVersion: 3.18
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data compSPOT |
| BuildTime: 0 minutes 44.35 seconds |
| CheckCommand: BiocCheckGitClone('compSPOT') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3079/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3079/ab0e0df39d69e5ff3b6dfad92c38e94e1ad0a321/compSPOT.install-out.txt compSPOT_0.99.10.tar.gz && BiocCheck('compSPOT_0.99.10.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 47.40 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh compSPOT_0.99.10.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 8.87 seconds |
| PackageFileSize: 2033.55 KiB |
| BuildID:: compSPOT_20230828192836 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: compSPOT. 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. Adding Build Product Information to Database.Checking Package status: 1. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘compSPOT/DESCRIPTION’ ... OK
* preparing ‘compSPOT’:
* 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 ‘compSPOT_0.99.10.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('compSPOT')
===============================
─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: compSPOT
─ PackageVersion: 0.99.10
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3079/ab0e0df39d69e5ff3b6dfad92c38e94e1ad0a321/compSPOT
─ 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/3079/ab0e0df39d69e5ff3b6dfad92c38e94e1ad0a321/compSPOT.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘compSPOT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘compSPOT’ version ‘0.99.10’
* 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 ‘compSPOT’ 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 ... WARNING
Dependence on R version ‘4.3.1’ not with patchlevel 0
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [1s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [9s/10s] NOTE
compare_features : count_mutations: no visible binding for global
variable ‘Sample’
compare_features : count_mutations: no visible binding for global
variable ‘Chromosome’
count_groups: no visible binding for global variable ‘Group’
count_mutations: no visible binding for global variable ‘Sample’
count_mutations: no visible binding for global variable ‘Chromosome’
find_hotspots: no visible binding for global variable ‘percent’
plot_ecdf: no visible binding for global variable ‘Hotspot’
plot_ecdf: no visible binding for global variable ‘Mutation_Count’
plot_ecdf: no visible binding for global variable ‘Group’
plot_features: no visible global function definition for ‘na.omit’
plot_features: no visible binding for global variable ‘Count’
plot_sigspot: no visible binding for global variable ‘percent’
plot_sigspot: no visible binding for global variable ‘number’
plot_sigspot: no visible binding for global variable ‘Label’
plot_sigspot: no visible binding for global variable ‘type’
plot_sigspot: no visible binding for global variable ‘Count’
plot_sigspot: no visible binding for global variable ‘Group’
plot_spot: no visible binding for global variable ‘Mutation_Count’
plot_spot: no visible binding for global variable ‘Hotspot’
plot_spot: no visible binding for global variable ‘Group’
region_counter: no visible binding for global variable ‘Sample’
region_counter: no visible binding for global variable ‘Chromosome’
spot_rank: no visible binding for global variable ‘Chromosome’
Undefined global functions or variables:
Chromosome Count Group Hotspot Label Mutation_Count Sample na.omit
number percent type
Consider adding
importFrom("stats", "na.omit")
to your NAMESPACE file.
* checking Rd files ... [0s/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 ... [0s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [141s/142s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
compare_groups 111.436 9.141 121.394
find_hotspots 12.016 1.090 13.173
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [16s/16s]
[16s/17s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
1. └─base::lapply(...) at test-check_features.R:4:0
2. └─compSPOT (local) FUN(X[[i]], ...)
3. └─stats::na.omit(df)
── Error ('test-check_groups.R:12:1'): (code run outside of `test_that()`) ─────
Error in `eval(code, test_env)`: object 'regions' not found
Backtrace:
▆
1. ├─data.table::rbindlist(lapply(seq_len(nrow(regions)), count_groups)) at test-check_groups.R:12:0
2. ├─base::lapply(seq_len(nrow(regions)), count_groups)
3. └─base::nrow(regions)
── Error ('test-check_ranking.R:17:1'): (code run outside of `test_that()`) ────
Error in `seq_len(nrow(ranked_regions))[[-length(seq_len(nrow(ranked_regions)))]]`: attempt to select more than one element in integerOneIndex
Backtrace:
▆
1. └─base::lapply(...) at test-check_ranking.R:17:0
── Error ('test-spots.R:6:1'): (code run outside of `test_that()`) ─────────────
Error in `sig.spots(data = example_mutations, regions = example_regions,
pvalue = pval, threshold = thres, include_genes = TRUE, rank = TRUE)`: could not find function "sig.spots"
[ FAIL 4 | WARN 0 | SKIP 0 | PASS 0 ]
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 ... [9s/10s] OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3079/ab0e0df39d69e5ff3b6dfad92c38e94e1ad0a321/compSPOT.Rcheck/00check.log’
for details.
===============================
BiocCheck('compSPOT_0.99.10.tar.gz')
===============================
─ BiocCheckVersion: 1.37.12
─ BiocVersion: 3.18
─ Package: compSPOT
─ PackageVersion: 0.99.10
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpSdXsXb/filed08d1aa4f571/compSPOT
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpSdXsXb/filed08d34dde01e
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3079/ab0e0df39d69e5ff3b6dfad92c38e94e1ad0a321/compSPOT.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...
* WARNING: Package files exceed the 5MB size limit.
* 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 compSPOT...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 6 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; 11 lines (1%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 360 lines
(19%) 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 | 1 WARNINGS | 3 NOTES
See the compSPOT.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir compSPOT_0.99.10.tar.gz'
>>>>>>>
* installing *source* package ‘compSPOT’ ...
** 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 (compSPOT)