nebbiolo2 Summary
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| Package: RNAseqCovarImpute |
| 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 RNAseqCovarImpute |
| BuildTime: 0 minutes 28.75 seconds |
| CheckCommand: BiocCheckGitClone('RNAseqCovarImpute') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3021/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3021/7c01e4a23291987715cb149debb144ac9e021e31/RNAseqCovarImpute.install-out.txt RNAseqCovarImpute_0.99.10.tar.gz && BiocCheck('RNAseqCovarImpute_0.99.10.tar.gz', `new-package`=TRUE) |
| CheckTime: 1 minutes 44.70 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 755.17 KiB |
| BuildID:: RNAseqCovarImpute_20231006204123 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: RNAseqCovarImpute. 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: 0. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘RNAseqCovarImpute/DESCRIPTION’ ... OK
* preparing ‘RNAseqCovarImpute’:
* 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 ‘RNAseqCovarImpute_0.99.10.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('RNAseqCovarImpute')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: RNAseqCovarImpute
─ PackageVersion: 0.99.10
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3021/7c01e4a23291987715cb149debb144ac9e021e31/RNAseqCovarImpute
─ 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/3021/7c01e4a23291987715cb149debb144ac9e021e31/RNAseqCovarImpute.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 ‘RNAseqCovarImpute/DESCRIPTION’ ... OK
* this is package ‘RNAseqCovarImpute’ 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 ‘RNAseqCovarImpute’ 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
Invalid license file pointers: LICENSE
* 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [10s/10s] NOTE
combine_rubins: no visible binding for global variable ‘i’
combine_rubins: no visible binding for global variable ‘coef_combined’
combine_rubins: no visible binding for global variable ‘rubins_t_bayes’
combine_rubins: no visible binding for global variable ‘combined_p’
combine_rubins: no visible binding for global variable
‘combined_p_bayes’
get_gene_bin_intervals: no visible binding for global variable ‘end’
get_gene_bin_intervals: no visible binding for global variable ‘start’
limmavoom_imputed_data_list_helper: no visible binding for global
variable ‘i’
lowess_all_gene_bins: no visible binding for global variable ‘gene_bin’
lowess_all_gene_bins: no visible binding for global variable ‘i’
voom_master_lowess: no visible global function definition for ‘is’
voom_master_lowess: no visible global function definition for ‘new’
voom_master_lowess: no visible global function definition for ‘lowess’
voom_master_lowess: no visible global function definition for
‘approxfun’
voom_sx_sy: no visible global function definition for ‘is’
voom_sx_sy: no visible global function definition for ‘new’
Undefined global functions or variables:
approxfun coef_combined combined_p combined_p_bayes end gene_bin i is
lowess new rubins_t_bayes start
Consider adding
importFrom("methods", "is", "new")
importFrom("stats", "approxfun", "end", "lowess", "start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/24s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
combine_rubins 9.021 0.666 5.601
limmavoom_imputed_data_list 8.262 0.631 4.634
impute_by_gene_bin 8.168 0.523 4.503
get_gene_bin_intervals 8.085 0.563 4.514
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [19s/16s]
[19s/16s] 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 ... [2s/2s] OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3021/7c01e4a23291987715cb149debb144ac9e021e31/RNAseqCovarImpute.Rcheck/00check.log’
for details.
===============================
BiocCheck('RNAseqCovarImpute_0.99.10.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: RNAseqCovarImpute
─ PackageVersion: 0.99.10
─ sourceDir: /tmp/RtmpJX7IQ8/file3ebcbab471df2/RNAseqCovarImpute
─ installDir: /tmp/RtmpJX7IQ8/file3ebcba22e4c4a5
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3021/7c01e4a23291987715cb149debb144ac9e021e31/RNAseqCovarImpute.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...
* NOTE: Consider adding these automatically suggested biocViews:
Bayesian
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* 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 RNAseqCovarImpute...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 3 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; 182 lines (12%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 33 lines (2%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 57 lines
(4%) 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 | 7 NOTES
See the RNAseqCovarImpute.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
[top]
lconway Summary
[top]
| Package: RNAseqCovarImpute |
| 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 RNAseqCovarImpute |
| BuildTime: 0 minutes 29.12 seconds |
| CheckCommand: BiocCheckGitClone('RNAseqCovarImpute') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3021/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3021/7c01e4a23291987715cb149debb144ac9e021e31/RNAseqCovarImpute.install-out.txt RNAseqCovarImpute_0.99.10.tar.gz && BiocCheck('RNAseqCovarImpute_0.99.10.tar.gz', `new-package`=TRUE) |
| CheckTime: 2 minutes 16.05 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh RNAseqCovarImpute_0.99.10.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 10.25 seconds |
| PackageFileSize: 754.97 KiB |
| BuildID:: RNAseqCovarImpute_20231006204123 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: RNAseqCovarImpute. 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: 0. Build Package status: 0. |
lconway BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘RNAseqCovarImpute/DESCRIPTION’ ... OK
* preparing ‘RNAseqCovarImpute’:
* 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 ‘RNAseqCovarImpute_0.99.10.tar.gz’
lconway CHECK output
[top]
===============================
BiocCheckGitClone('RNAseqCovarImpute')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: RNAseqCovarImpute
─ PackageVersion: 0.99.10
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3021/7c01e4a23291987715cb149debb144ac9e021e31/RNAseqCovarImpute
─ 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/3021/7c01e4a23291987715cb149debb144ac9e021e31/RNAseqCovarImpute.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 ‘RNAseqCovarImpute/DESCRIPTION’ ... OK
* this is package ‘RNAseqCovarImpute’ 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 ‘RNAseqCovarImpute’ 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
Invalid license file pointers: LICENSE
* 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 ... [3s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/5s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [11s/12s] NOTE
combine_rubins: no visible binding for global variable ‘i’
combine_rubins: no visible binding for global variable ‘coef_combined’
combine_rubins: no visible binding for global variable ‘rubins_t_bayes’
combine_rubins: no visible binding for global variable ‘combined_p’
combine_rubins: no visible binding for global variable
‘combined_p_bayes’
get_gene_bin_intervals: no visible binding for global variable ‘end’
get_gene_bin_intervals: no visible binding for global variable ‘start’
limmavoom_imputed_data_list_helper: no visible binding for global
variable ‘i’
lowess_all_gene_bins: no visible binding for global variable ‘gene_bin’
lowess_all_gene_bins: no visible binding for global variable ‘i’
voom_master_lowess: no visible global function definition for ‘is’
voom_master_lowess: no visible global function definition for ‘new’
voom_master_lowess: no visible global function definition for ‘lowess’
voom_master_lowess: no visible global function definition for
‘approxfun’
voom_sx_sy: no visible global function definition for ‘is’
voom_sx_sy: no visible global function definition for ‘new’
Undefined global functions or variables:
approxfun coef_combined combined_p combined_p_bayes end gene_bin i is
lowess new rubins_t_bayes start
Consider adding
importFrom("methods", "is", "new")
importFrom("stats", "approxfun", "end", "lowess", "start")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [40s/24s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
combine_rubins 8.749 1.210 5.753
get_gene_bin_intervals 7.881 1.130 4.739
limmavoom_imputed_data_list 7.424 1.068 4.454
impute_by_gene_bin 7.421 1.051 4.447
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [20s/17s]
[20s/17s] 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 ... [6s/6s] OK
* DONE
Status: 1 WARNING, 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3021/7c01e4a23291987715cb149debb144ac9e021e31/RNAseqCovarImpute.Rcheck/00check.log’
for details.
===============================
BiocCheck('RNAseqCovarImpute_0.99.10.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: RNAseqCovarImpute
─ PackageVersion: 0.99.10
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpxWl43b/file5f222ccd8845/RNAseqCovarImpute
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpxWl43b/file5f227def983e
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3021/7c01e4a23291987715cb149debb144ac9e021e31/RNAseqCovarImpute.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...
* NOTE: Consider adding these automatically suggested biocViews:
Bayesian
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* 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 RNAseqCovarImpute...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 3 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; 182 lines (12%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 33 lines (2%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 57 lines
(4%) 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 | 7 NOTES
See the RNAseqCovarImpute.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 RNAseqCovarImpute_0.99.10.tar.gz'
>>>>>>>
* installing *source* package ‘RNAseqCovarImpute’ ...
** 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 (RNAseqCovarImpute)