machv2 Summary
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| Package: Magellan |
| Version: 0.99.1 |
| RVersion: 4.1
|
| BiocVersion: 3.13
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data Magellan |
| BuildTime: 0 minutes 27.35 seconds |
| CheckCommand: BiocCheckGitClone('Magellan') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch Magellan_0.99.1.tar.gz && BiocCheck('Magellan_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 4.41 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh Magellan_0.99.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 24.91 seconds |
| PackageFileSize: 848.95 KiB |
| BuildID:: Magellan_20210607193621 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: Magellan. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 1. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. Build Package status: 0. |
machv2 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘Magellan/DESCRIPTION’ ... OK
* preparing ‘Magellan’:
* 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 ‘Magellan_0.99.1.tar.gz’
machv2 CHECK output
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===============================
BiocCheckGitClone('Magellan')
===============================
This is BiocCheckGitClone version 1.29.7. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
Magellan.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2129/Magellan_20210607193621/Magellan.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Magellan/DESCRIPTION’ ... OK
* this is package ‘Magellan’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package suggested but not available: ‘MSPipelines’
The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2129/Magellan_20210607193621/Magellan.Rcheck/00check.log’
for details.
===============================
BiocCheck('Magellan_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.29.7. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
Warning: replacing previous import ‘DT::dataTableOutput’ by ‘shiny::dataTableOutput’ when loading ‘Magellan’
Warning: replacing previous import ‘DT::renderDataTable’ by ‘shiny::renderDataTable’ when loading ‘Magellan’
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 25 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
function (object)
app_server (hlpsms)
app_server (Protein)
mod_nav_pipeline_server (dataOut)
mod_nav_pipeline_server (GetStringStatus)
mod_nav_pipeline_server (setNames)
mod_nav_pipeline_server (CheckConfig)
mod_nav_pipeline_server (setNames)
mod_nav_pipeline_server (GetMaxValidated_AllSteps)
mod_nav_pipeline_server (GetFirstMandatoryNotValidated)
mod_nav_pipeline_server (Change_Current_Pos)
mod_nav_pipeline_server (GetMaxValidated_BeforeCurrentPos)
mod_nav_pipeline_server (setNames)
mod_nav_pipeline_server (blue)
mod_nav_pipeline_server (setNames)
mod_nav_pipeline_server (blue)
mod_nav_pipeline_server (Discover_Skipped_Steps)
mod_nav_pipeline_server (Timestamp)
mod_nav_process_server (GetStringStatus)
mod_nav_process_server (CheckConfig)
mod_nav_process_server (setNames)
mod_nav_process_server (Discover_Skipped_Steps)
mod_nav_process_server (GetMaxValidated_AllSteps)
mod_nav_process_server (GetFirstMandatoryNotValidated)
mod_nav_process_server (Change_Current_Pos)
mod_nav_process_server (setNames)
* 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 DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
CreatePipeline.Rmd
Magellan.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Magellan...
* Checking coding practice...
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/R/mod_nav_pipeline.R
(line 394, column 21)
/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/R/mod_nav_process.R
(line 309, column 21)
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/app_pipeline.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/app_process_light.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/app_process.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/auto_launch_2.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/auto_launch_process.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/dash_example.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/dash_Magellan_example.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/Example_Description.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/Example_ProcessA.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/Example_ProcessB.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/Example_ProcessC.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/Example.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/integrate_a_pipeline_package.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/NewStart_Magellan_Lead/dash_example.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/NewStart_Magellan_Lead/mod_nav_pipeline.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/NewStart_Magellan_Lead/mod_nav_process.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/NewStart_Magellan_Lead/test_mod_convert.R'
Warning in readLines(infile) :
incomplete final line found on '/var/folders/xd/gpmk_x0977q95yv9tx6z_pqm0000gv/T//RtmpMvvQS9/file7d7429ca361b/Magellan/dev/test_dev/NewStart_Magellan_Lead/test_mod_ext_Process.R'
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths.........................
* NOTE: Recommended function length <= 50 lines.
There are 11 functions > 50 lines.
The longest 5 functions are:
mod_nav_pipeline_server() (R/mod_nav_pipeline.R, line 155): 728
lines
_anonymous_.168() (R/mod_nav_pipeline.R, line 168): 713 lines
mod_nav_process_server() (R/mod_nav_process.R, line 110): 514
lines
_anonymous_.123() (R/mod_nav_process.R, line 123): 499 lines
mod_timeline_v_server() (R/mod_timeline_v.R, line 61): 152
lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
run_app.Rd
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 195 lines (6%) are > 80 characters
long.
First 6 lines:
R/mod_bsmodal.R:68 tags$head(tags$style("#test .modal-dialog {w...
R/mod_format_DT.R:88 columnDefs = l...
R/mod_format_DT.R:102 columnDefs = ...
R/mod_format_DT.R:120 "$(this.api().table().header()).css({'bac...
R/mod_nav_pipeline.R:172 source(system.file("extdata", 'commonFuncs...
R/mod_nav_pipeline.R:205 #if (verbose) cat(paste0(class(self)[1],...
* NOTE: Consider multiples of 4 spaces for line indents, 1016
lines(32%) are not.
First 6 lines:
R/app_config.R:8 system.file(..., package = "Magellan")
R/app_config.R:22 value,
R/app_config.R:23 config = Sys.getenv("R_CONFIG_ACTIVE", "default"),
R/app_config.R:24 use_parent = TRUE
R/app_config.R:26 config::get(
R/app_config.R:32 )
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: 8
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
machv2 BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir Magellan_0.99.1.tar.gz'
>>>>>>>
* installing *source* package ‘Magellan’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘DT::dataTableOutput’ by ‘shiny::dataTableOutput’ when loading ‘Magellan’
Warning: replacing previous import ‘DT::renderDataTable’ by ‘shiny::renderDataTable’ when loading ‘Magellan’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘DT::dataTableOutput’ by ‘shiny::dataTableOutput’ when loading ‘Magellan’
Warning: replacing previous import ‘DT::renderDataTable’ by ‘shiny::renderDataTable’ when loading ‘Magellan’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘DT::dataTableOutput’ by ‘shiny::dataTableOutput’ when loading ‘Magellan’
Warning: replacing previous import ‘DT::renderDataTable’ by ‘shiny::renderDataTable’ when loading ‘Magellan’
** testing if installed package keeps a record of temporary installation path
* DONE (Magellan)
malbec2 Summary
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| Package: Magellan |
| Version: 0.99.1 |
| RVersion: 4.1
|
| BiocVersion: 3.13
|
| BuildCommand: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Magellan |
| BuildTime: 0 minutes 23.90 seconds |
| CheckCommand: BiocCheckGitClone('Magellan') && /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --no-vignettes --timings Magellan_0.99.1.tar.gz && BiocCheck('Magellan_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 4.04 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 848.95 KiB |
| BuildID:: Magellan_20210607193621 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: Magellan. Starting Build package. Starting Check package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 1. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 1. |
malbec2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘Magellan/DESCRIPTION’ ... OK
* preparing ‘Magellan’:
* 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 ‘Magellan_0.99.1.tar.gz’
malbec2 CHECK output
[top]
===============================
BiocCheckGitClone('Magellan')
===============================
This is BiocCheckGitClone version 1.29.7. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
Magellan.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2129/Magellan_20210607193621/Magellan.Rcheck’
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Magellan/DESCRIPTION’ ... OK
* this is package ‘Magellan’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package suggested but not available: ‘MSPipelines’
The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2129/Magellan_20210607193621/Magellan.Rcheck/00check.log’
for details.
===============================
BiocCheck('Magellan_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.29.7. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
Warning: replacing previous import ‘DT::dataTableOutput’ by ‘shiny::dataTableOutput’ when loading ‘Magellan’
Warning: replacing previous import ‘DT::renderDataTable’ by ‘shiny::renderDataTable’ when loading ‘Magellan’
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 25 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
function (object)
app_server (hlpsms)
app_server (Protein)
mod_nav_pipeline_server (dataOut)
mod_nav_pipeline_server (GetStringStatus)
mod_nav_pipeline_server (setNames)
mod_nav_pipeline_server (CheckConfig)
mod_nav_pipeline_server (setNames)
mod_nav_pipeline_server (GetMaxValidated_AllSteps)
mod_nav_pipeline_server (GetFirstMandatoryNotValidated)
mod_nav_pipeline_server (Change_Current_Pos)
mod_nav_pipeline_server (GetMaxValidated_BeforeCurrentPos)
mod_nav_pipeline_server (setNames)
mod_nav_pipeline_server (blue)
mod_nav_pipeline_server (setNames)
mod_nav_pipeline_server (blue)
mod_nav_pipeline_server (Discover_Skipped_Steps)
mod_nav_pipeline_server (Timestamp)
mod_nav_process_server (GetStringStatus)
mod_nav_process_server (CheckConfig)
mod_nav_process_server (setNames)
mod_nav_process_server (Discover_Skipped_Steps)
mod_nav_process_server (GetMaxValidated_AllSteps)
mod_nav_process_server (GetFirstMandatoryNotValidated)
mod_nav_process_server (Change_Current_Pos)
mod_nav_process_server (setNames)
* 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 DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
CreatePipeline.Rmd
Magellan.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Magellan...
* Checking coding practice...
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/R/mod_nav_pipeline.R
(line 394, column 21)
/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/R/mod_nav_process.R
(line 309, column 21)
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/app_pipeline.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/app_process_light.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/app_process.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/auto_launch_2.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/auto_launch_process.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/dash_example.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/dash_Magellan_example.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/Example_Description.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/Example_ProcessA.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/Example_ProcessB.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/Example_ProcessC.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/Example.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/integrate_a_pipeline_package.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/NewStart_Magellan_Lead/dash_example.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/NewStart_Magellan_Lead/mod_nav_pipeline.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/NewStart_Magellan_Lead/mod_nav_process.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/NewStart_Magellan_Lead/test_mod_convert.R'
Warning in readLines(infile) :
incomplete final line found on '/tmp/RtmpzEdzql/filec741227fe26d5/Magellan/dev/test_dev/NewStart_Magellan_Lead/test_mod_ext_Process.R'
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths.........................
* NOTE: Recommended function length <= 50 lines.
There are 11 functions > 50 lines.
The longest 5 functions are:
mod_nav_pipeline_server() (R/mod_nav_pipeline.R, line 155): 728
lines
_anonymous_.168() (R/mod_nav_pipeline.R, line 168): 713 lines
mod_nav_process_server() (R/mod_nav_process.R, line 110): 514
lines
_anonymous_.123() (R/mod_nav_process.R, line 123): 499 lines
mod_timeline_v_server() (R/mod_timeline_v.R, line 61): 152
lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
run_app.Rd
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 195 lines (6%) are > 80 characters
long.
First 6 lines:
R/mod_bsmodal.R:68 tags$head(tags$style("#test .modal-dialog {w...
R/mod_format_DT.R:88 columnDefs = l...
R/mod_format_DT.R:102 columnDefs = ...
R/mod_format_DT.R:120 "$(this.api().table().header()).css({'bac...
R/mod_nav_pipeline.R:172 source(system.file("extdata", 'commonFuncs...
R/mod_nav_pipeline.R:205 #if (verbose) cat(paste0(class(self)[1],...
* NOTE: Consider multiples of 4 spaces for line indents, 1016
lines(32%) are not.
First 6 lines:
R/app_config.R:8 system.file(..., package = "Magellan")
R/app_config.R:22 value,
R/app_config.R:23 config = Sys.getenv("R_CONFIG_ACTIVE", "default"),
R/app_config.R:24 use_parent = TRUE
R/app_config.R:26 config::get(
R/app_config.R:32 )
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: 8
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
malbec2 BUILD BIN output
[top]
tokay2 Summary
[top]
| Package: Magellan |
| Version: 0.99.1 |
| RVersion: 4.1
|
| BiocVersion: 3.13
|
| BuildCommand: C:\Users\biocbuild\bbs-3.13-bioc\R\bin/R CMD build --keep-empty-dirs --no-resave-data Magellan |
| BuildTime: 0 minutes 32.07 seconds |
| CheckCommand: C:\Users\biocbuild\bbs-3.13-bioc\R\bin/R CMD INSTALL --build --merge-multiarch --library=Magellan.buildbin-libdir Magellan_0.99.1.tar.gz >Magellan-install.out 2>&1 && C:\Users\biocbuild\bbs-3.13-bioc\R\bin/R CMD check --library=Magellan.buildbin-libdir --install="check:Magellan-install.out" --force-multiarch --no-vignettes --timings Magellan_0.99.1.tar.gz && BiocCheck('Magellan_0.99.1.tar.gz', `new-package`=TRUE) |
| CheckTime: 0 minutes 4.87 seconds |
| BuildBinCommand: C:\Users\biocbuild\bbs-3.13-bioc\R\bin/R CMD INSTALL --build --merge-multiarch --library=Magellan.buildbin-libdir Magellan_0.99.1.tar.gz |
| BuildBinTime: 0 minutes 32.14 seconds |
| PackageFileSize: 849.79 KiB |
| BuildID:: Magellan_20210607193621 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: Magellan. Starting Build package. Starting Check package. Starting Build package. |
| PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 1. Checking git clone status: 1. Installing package status: 0. Build Package status: 0. Checking Package status: 0. Build Package status: 0. |
tokay2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file 'Magellan/DESCRIPTION' ... OK
* preparing 'Magellan':
* 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 'Magellan_0.99.1.tar.gz'
tokay2 CHECK output
[top]
Installing package prior to check...
===============================
BiocCheckGitClone('Magellan')
===============================
This is BiocCheckGitClone version 1.29.7. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* ERROR: System Files found that should not be git tracked:
Magellan.Rproj
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory 'C:/Users/pkgbuild/packagebuilder/workers/jobs/2129/Magellan_20210607193621/Magellan.Rcheck'
* using R version 4.1.0 (2021-05-18)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'Magellan/DESCRIPTION' ... OK
* this is package 'Magellan' version '0.99.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package suggested but not available: 'MSPipelines'
The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
* DONE
Status: 1 ERROR
See
'C:/Users/pkgbuild/packagebuilder/workers/jobs/2129/Magellan_20210607193621/Magellan.Rcheck/00check.log'
for details.
===============================
BiocCheck('Magellan_0.99.1.tar.gz')
===============================
This is BiocCheck version 1.29.7. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
Warning: replacing previous import 'DT::dataTableOutput' by 'shiny::dataTableOutput' when loading 'Magellan'
Warning: replacing previous import 'DT::renderDataTable' by 'shiny::renderDataTable' when loading 'Magellan'
* Checking Package Dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* NOTE: Consider clarifying how 25 object(s) are initialized. Maybe
they are part of a data set loaded with data(), or perhaps part
of an object referenced in with() or within().
function (object)
app_server (hlpsms)
app_server (Protein)
mod_nav_pipeline_server (dataOut)
mod_nav_pipeline_server (GetStringStatus)
mod_nav_pipeline_server (setNames)
mod_nav_pipeline_server (CheckConfig)
mod_nav_pipeline_server (setNames)
mod_nav_pipeline_server (GetMaxValidated_AllSteps)
mod_nav_pipeline_server (GetFirstMandatoryNotValidated)
mod_nav_pipeline_server (Change_Current_Pos)
mod_nav_pipeline_server (GetMaxValidated_BeforeCurrentPos)
mod_nav_pipeline_server (setNames)
mod_nav_pipeline_server (blue)
mod_nav_pipeline_server (setNames)
mod_nav_pipeline_server (blue)
mod_nav_pipeline_server (Discover_Skipped_Steps)
mod_nav_pipeline_server (Timestamp)
mod_nav_process_server (GetStringStatus)
mod_nav_process_server (CheckConfig)
mod_nav_process_server (setNames)
mod_nav_process_server (Discover_Skipped_Steps)
mod_nav_process_server (GetMaxValidated_AllSteps)
mod_nav_process_server (GetFirstMandatoryNotValidated)
mod_nav_process_server (Change_Current_Pos)
mod_nav_process_server (setNames)
* 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 DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
CreatePipeline.Rmd
Magellan.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of Magellan...
* Checking coding practice...
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/R/mod_nav_pipeline.R
(line 394, column 21)
C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/R/mod_nav_process.R
(line 309, column 21)
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/app_pipeline.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/app_process.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/app_process_light.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/auto_launch_2.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/auto_launch_process.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/dash_example.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/dash_Magellan_example.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/Example.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/Example_Description.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/Example_ProcessA.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/Example_ProcessB.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/Example_ProcessC.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/integrate_a_pipeline_package.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/NewStart_Magellan_Lead/dash_example.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/NewStart_Magellan_Lead/mod_nav_pipeline.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/NewStart_Magellan_Lead/mod_nav_process.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/NewStart_Magellan_Lead/test_mod_convert.R'
Warning in readLines(infile) :
incomplete final line found on 'C:\Users\pkgbuild\AppData\Local\Temp\RtmpMZQXWK\file72e060c25749/Magellan/dev/test_dev/NewStart_Magellan_Lead/test_mod_ext_Process.R'
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths.........................
* NOTE: Recommended function length <= 50 lines.
There are 11 functions > 50 lines.
The longest 5 functions are:
mod_nav_pipeline_server() (R/mod_nav_pipeline.R, line 155): 728
lines
_anonymous_.168() (R/mod_nav_pipeline.R, line 168): 713 lines
mod_nav_process_server() (R/mod_nav_process.R, line 110): 514
lines
_anonymous_.123() (R/mod_nav_process.R, line 123): 499 lines
mod_timeline_v_server() (R/mod_timeline_v.R, line 61): 152
lines
* Checking man page documentation...
* NOTE: Consider adding runnable examples to the following man
pages which document exported objects:
run_app.Rd
* Checking package NEWS...
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 195 lines (6%) are > 80 characters
long.
First 6 lines:
R/mod_bsmodal.R:68 tags$head(tags$style("#test .modal-dialog {w...
R/mod_format_DT.R:88 columnDefs = l...
R/mod_format_DT.R:102 columnDefs = ...
R/mod_format_DT.R:120 "$(this.api().table().header()).css({'bac...
R/mod_nav_pipeline.R:172 source(system.file("extdata", 'commonFuncs...
R/mod_nav_pipeline.R:205 #if (verbose) cat(paste0(class(self)[1],...
* NOTE: Consider multiples of 4 spaces for line indents, 1016
lines(32%) are not.
First 6 lines:
R/app_config.R:8 system.file(..., package = "Magellan")
R/app_config.R:22 value,
R/app_config.R:23 config = Sys.getenv("R_CONFIG_ACTIVE", "default"),
R/app_config.R:24 use_parent = TRUE
R/app_config.R:26 config::get(
R/app_config.R:32 )
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: 8
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.13/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
tokay2 BUILD BIN output
[top]
===============================
R CMD BUILD
===============================
install for i386
* installing *source* package 'Magellan' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'DT::dataTableOutput' by 'shiny::dataTableOutput' when loading 'Magellan'
Warning: replacing previous import 'DT::renderDataTable' by 'shiny::renderDataTable' when loading 'Magellan'
** help
*** installing help indices
converting help for package 'Magellan'
finding HTML links ... done
Add_Item_to_Dataset html
Keep_Items_from_Dataset html
Send_Result_to_Caller html
mod_bsmodal_server html
mod_format_DT html
mod_nav_pipeline_server html
mod_nav_process_server html
mod_popover_for_help html
mod_timeline_h_server html
mod_timeline_v_server html
run_app html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'DT::dataTableOutput' by 'shiny::dataTableOutput' when loading 'Magellan'
Warning: replacing previous import 'DT::renderDataTable' by 'shiny::renderDataTable' when loading 'Magellan'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'DT::dataTableOutput' by 'shiny::dataTableOutput' when loading 'Magellan'
Warning: replacing previous import 'DT::renderDataTable' by 'shiny::renderDataTable' when loading 'Magellan'
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'Magellan' ...
** testing if installed package can be loaded
Warning: replacing previous import 'DT::dataTableOutput' by 'shiny::dataTableOutput' when loading 'Magellan'
Warning: replacing previous import 'DT::renderDataTable' by 'shiny::renderDataTable' when loading 'Magellan'
* MD5 sums
packaged installation of 'Magellan' as Magellan_0.99.1.zip
* DONE (Magellan)