merida1 Summary
[top]
Package: omicsViewer |
Version: 0.99.16 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data omicsViewer |
BuildTime: 3 minutes 35.85 seconds |
CheckCommand: BiocCheckGitClone('omicsViewer') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch omicsViewer_0.99.16.tar.gz && BiocCheck('omicsViewer_0.99.16.tar.gz', `new-package`=TRUE) |
CheckTime: 14 minutes 59.96 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh omicsViewer_0.99.16.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 2 minutes 19.41 seconds |
PackageFileSize: 4394.50 KiB |
BuildID:: omicsViewer_20220325132713 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: omicsViewer. 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. Checking Package status: -9. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘omicsViewer/DESCRIPTION’ ... OK
* preparing ‘omicsViewer’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘omicsViewer_0.99.16.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('omicsViewer')
===============================
This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2523/5a8d380cfe685110d7c7a23801cada66e8cfb71a/omicsViewer.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘omicsViewer/DESCRIPTION’ ... OK
* this is package ‘omicsViewer’ version ‘0.99.16’
* 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘omicsViewer’ can be installed ... [65s/143s] OK
* checking installed package size ... NOTE
installed size is 6.2Mb
sub-directories of 1Mb or more:
extdata 4.8Mb
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [78s/199s] NOTE
Found the following assignments to the global environment:
File ‘omicsViewer/R/module_scatter.R’:
assign(figureId(), fata, envir = .GlobalEnv)
* 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 ... ERROR
TIMEOUT: R CMD check exceeded 14 mins
===============================
BiocCheck('omicsViewer_0.99.16.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
OK
* checking Rd \usage sections ...* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2523/5a8d380cfe685110d7c7a23801cada66e8cfb71a/omicsViewer_0.99.16.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpijJbbu/file12b2d3c2a2e98/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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 4.1 to 4.2.0.
* Checking package size...
OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ...* Checking individual file sizes...
OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...* 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 vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of omicsViewer...
* Checking coding practice...
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/auxi_queryStringdb.R (line 66, column 13)
R/auxi_queryStringdb.R (line 158, column 13)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8
times)
suppressWarnings() in R/auxi_figureAttr4.R (line 97, column 9)
suppressMessages() in R/auxi_queryStringdb.R (line 58, column
9)
suppressMessages() in R/auxi_queryStringdb.R (line 98, column
3)
suppressMessages() in R/auxi_queryStringdb.R (line 148, column
9)
suppressWarnings() in R/module_contTableStats.R (line 14,
column 3)
suppressWarnings() in R/module_scatter.R (line 487, column 5)
suppressWarnings() in R/module_scatter.R (line 534, column 5)
suppressWarnings() in R/module_survival.R (line 83, column 5)
* Checking function lengths...
[52s/118s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
multi.t.test 7.228 0.21 17.416
prepOmicsViewer 6.292 0.11 11.812
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test_auxi_sparse_converter.R’ * NOTE: Recommended function length <= 50 lines.
There are 33 functions > 50 lines.
The longest 5 functions are:
iheatmapModule() (R/heatmapshinyApp.R, line 180): 633 lines
app_module() (R/L0_module_app.R, line 108): 306 lines
meta_scatter_module() (R/module_meta_scatter.R, line 53): 237
lines
prepOmicsViewer() (R/00_export_prepEsetViewer.R, line 72): 198
lines
L1_data_space_module() (R/L1_module_data_space.R, line 87): 198
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; 850 lines (8%) are > 80 characters
long.
First 6 lines:
R/00_export_getAutoRIF.R:16 #' Nucleic Acids Research, Volume 47, Iss...
R/00_export_getAutoRIF.R:23 getAutoRIF <- function(term, rif = c("gener...
R/00_export_prepEsetViewer.R:2 #' @description This is a convenience fu...
R/00_export_prepEsetViewer.R:4 #' @param expr expression matrix where t...
R/00_export_prepEsetViewer.R:10 #' @param pca.fillNA logical, whether t...
R/00_export_prepEsetViewer.R:11 #' @param t.test will be passed to the ...
* NOTE: Consider multiples of 4 spaces for line indents, 3665
lines(34%) are not.
First 6 lines:
R/00_export_getAutoRIF.R:24 term <- gsub(" ", "%20", term)
R/00_export_getAutoRIF.R:25 term <- paste(term, collapse = ",")
R/00_export_getAutoRIF.R:26 GENESHOT_URL <- 'https://maayanlab.cloud/...
R/00_export_getAutoRIF.R:27 payload <- list("rif" = rif, "term" = term)
R/00_export_getAutoRIF.R:28 r <- httr::POST(GENESHOT_URL, body = payl...
R/00_export_getAutoRIF.R:29 r <- httr::content(r)
See http://bioconductor.org/developers/how-to/coding-style/
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.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 6
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
merida1 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir omicsViewer_0.99.16.tar.gz'
>>>>>>>
* installing *source* package ‘omicsViewer’ ...
** using staged installation
** R
** 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 (omicsViewer)
nebbiolo1 Summary
[top]
Package: omicsViewer |
Version: 0.99.16 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data omicsViewer |
BuildTime: 0 minutes 32.89 seconds |
CheckCommand: BiocCheckGitClone('omicsViewer') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings omicsViewer_0.99.16.tar.gz && BiocCheck('omicsViewer_0.99.16.tar.gz', `new-package`=TRUE) |
CheckTime: 3 minutes 9.12 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 4395.30 KiB |
BuildID:: omicsViewer_20220325132713 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: omicsViewer. 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. Checking Package status: 0. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘omicsViewer/DESCRIPTION’ ... OK
* preparing ‘omicsViewer’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘omicsViewer_0.99.16.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('omicsViewer')
===============================
This is BiocCheckGitClone version 1.31.36. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2523/5a8d380cfe685110d7c7a23801cada66e8cfb71a/omicsViewer.Rcheck’
* using R Under development (unstable) (2022-03-17 r81925)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘omicsViewer/DESCRIPTION’ ... OK
* this is package ‘omicsViewer’ version ‘0.99.16’
* 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘omicsViewer’ can be installed ... [24s/24s] OK
* checking installed package size ... NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
extdata 4.2Mb
* 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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [24s/24s] NOTE
Found the following assignments to the global environment:
File ‘omicsViewer/R/module_scatter.R’:
assign(figureId(), fata, envir = .GlobalEnv)
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [23s/24s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘test_auxi_sparse_converter.R’ [6s/6s]
[6s/6s] 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 ... OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2523/5a8d380cfe685110d7c7a23801cada66e8cfb71a/omicsViewer.Rcheck/00check.log’
for details.
===============================
BiocCheck('omicsViewer_0.99.16.tar.gz')
===============================
This is BiocCheck version 1.31.36. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/home/biocbuild/bbs-3.15-bioc/R/bin/R' -q --vanilla --slave -f /home/biocbuild/bbs-3.15-bioc/R/library/BiocCheck/script/checkBadDeps.R --args "/home/pkgbuild/packagebuilder/workers/jobs/2523/5a8d380cfe685110d7c7a23801cada66e8cfb71a/omicsViewer_0.99.16.tar.gz" "/tmp/RtmpBH4fzw/file4a57a16d5ef57/lib" 2>/dev/null' had status 1
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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 4.1 to 4.2.0.
* 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 pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Warning in for (i in seq_len(n)) { :
closing unused connection 3 (http://bioconductor.org/js/versions.js)
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of omicsViewer...
* Checking coding practice...
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/auxi_queryStringdb.R (line 66, column 13)
R/auxi_queryStringdb.R (line 158, column 13)
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 8
times)
suppressWarnings() in R/auxi_figureAttr4.R (line 97, column 9)
suppressMessages() in R/auxi_queryStringdb.R (line 58, column
9)
suppressMessages() in R/auxi_queryStringdb.R (line 98, column
3)
suppressMessages() in R/auxi_queryStringdb.R (line 148, column
9)
suppressWarnings() in R/module_contTableStats.R (line 14,
column 3)
suppressWarnings() in R/module_scatter.R (line 487, column 5)
suppressWarnings() in R/module_scatter.R (line 534, column 5)
suppressWarnings() in R/module_survival.R (line 83, column 5)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 33 functions > 50 lines.
The longest 5 functions are:
iheatmapModule() (R/heatmapshinyApp.R, line 180): 633 lines
app_module() (R/L0_module_app.R, line 108): 306 lines
meta_scatter_module() (R/module_meta_scatter.R, line 53): 237
lines
prepOmicsViewer() (R/00_export_prepEsetViewer.R, line 72): 198
lines
L1_data_space_module() (R/L1_module_data_space.R, line 87): 198
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; 850 lines (8%) are > 80 characters
long.
First 6 lines:
R/00_export_getAutoRIF.R:16 #' Nucleic Acids Research, Volume 47, Iss...
R/00_export_getAutoRIF.R:23 getAutoRIF <- function(term, rif = c("gener...
R/00_export_prepEsetViewer.R:2 #' @description This is a convenience fu...
R/00_export_prepEsetViewer.R:4 #' @param expr expression matrix where t...
R/00_export_prepEsetViewer.R:10 #' @param pca.fillNA logical, whether t...
R/00_export_prepEsetViewer.R:11 #' @param t.test will be passed to the ...
* NOTE: Consider multiples of 4 spaces for line indents, 3665
lines(34%) are not.
First 6 lines:
R/00_export_getAutoRIF.R:24 term <- gsub(" ", "%20", term)
R/00_export_getAutoRIF.R:25 term <- paste(term, collapse = ",")
R/00_export_getAutoRIF.R:26 GENESHOT_URL <- 'https://maayanlab.cloud/...
R/00_export_getAutoRIF.R:27 payload <- list("rif" = rif, "term" = term)
R/00_export_getAutoRIF.R:28 r <- httr::POST(GENESHOT_URL, body = payl...
R/00_export_getAutoRIF.R:29 r <- httr::content(r)
See http://bioconductor.org/developers/how-to/coding-style/
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.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 6
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
nebbiolo1 BUILD BIN output
[top]