merida1 Summary
[top]
| Package: standR |
| Version: 0.99.9 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data standR |
| BuildTime: 5 minutes 43.23 seconds |
| CheckCommand: BiocCheckGitClone('standR') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch standR_0.99.9.tar.gz && BiocCheck('standR_0.99.9.tar.gz', `new-package`=TRUE) |
| CheckTime: 9 minutes 49.82 seconds |
| BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh standR_0.99.9.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
| BuildBinTime: 0 minutes 53.38 seconds |
| PackageFileSize: 3232.59 KiB |
| BuildID:: standR_20220409102928 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: standR. 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: 1. Build Package status: 0. |
merida1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘standR/DESCRIPTION’ ... OK
* preparing ‘standR’:
* 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 ‘standR_0.99.9.tar.gz’
merida1 CHECK output
[top]
===============================
BiocCheckGitClone('standR')
===============================
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/2574/4de64716797d6328047118e13ee365b45dd3c070/standR.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 ‘standR/DESCRIPTION’ ... OK
* this is package ‘standR’ version ‘0.99.9’
* 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 ‘standR’ can be installed ... [41s/42s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... 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 ... [49s/51s] OK
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [48s/49s] ERROR
Running examples in ‘standR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geomxNorm
> ### Title: Perform normalization to GeoMX data
> ### Aliases: geomxNorm
>
> ### ** Examples
>
> data("dkd_spe_subset")
>
> spe_tmm <- geomxNorm(dkd_spe_subset, method = "TMM")
> head(assay(spe_tmm, "logcounts"))
Error in assay(spe_tmm, "logcounts") : could not find function "assay"
Calls: head
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [115s/165s]
[115s/166s] 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: 1 ERROR
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/2574/4de64716797d6328047118e13ee365b45dd3c070/standR.Rcheck/00check.log’
for details.
===============================
BiocCheck('standR_0.99.9.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 '/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/2574/4de64716797d6328047118e13ee365b45dd3c070/standR_0.99.9.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//Rtmpm4R88N/file31216b299a4a/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...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of standR...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/plotGeneQCs.R (line 46, column 10)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 5 functions > 50 lines.
The longest 5 functions are:
geomx_import_fun() (R/geomx_import_data.R, line 38): 109 lines
plotPCAbiplot() (R/pcaOtherPlotting.R, line 170): 74 lines
plotROIQC() (R/plotLibQC.R, line 33): 69 lines
geomxNorm() (R/normalisation.R, line 50): 68 lines
plotPairPCA() (R/pcaOtherPlotting.R, line 30): 65 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; 165 lines (5%) are > 80 characters
long.
First 6 lines:
R/addQCstat.R:4 #' @param sample_fraction Double. Genes with low count ...
R/addQCstat.R:5 #' @param rm_genes Logical. Decide whether genes with l...
R/addQCstat.R:6 #' @param min_count Integer. Minimum read count to calc...
R/addQCstat.R:7 #' @param design Generate using `model.matrix`, if this...
R/addQCstat.R:17 addPerROIQC <- function(spe_object, sample_fraction = ...
R/addQCstat.R:37 ###### Genes with low count in more than the thresho...
* NOTE: Consider multiples of 4 spaces for line indents, 797
lines(23%) are not.
First 6 lines:
R/addQCstat.R:18 spe <- spe_object
R/addQCstat.R:20 stopifnot(nrow(spe) > 0)
R/addQCstat.R:21 stopifnot(ncol(spe) > 0)
R/addQCstat.R:22 stopifnot(length(SummarizedExperiment::assayNames(sp...
R/addQCstat.R:23 stopifnot(sample_fraction <= 1 & sample_fraction >= 0)
R/addQCstat.R:24 stopifnot(min_count >= 0)
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: 4
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
[top]
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir standR_0.99.9.tar.gz'
>>>>>>>
* installing *source* package ‘standR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
in method for ‘drawPCA’ with signature ‘"DGEList"’: no definition for class “DGEList”
in method for ‘drawPCA’ with signature ‘"SpatialExperiment"’: no definition for class “SpatialExperiment”
in method for ‘plotDR’ with signature ‘"SpatialExperiment","ANY"’: no definition for class “SpatialExperiment”
in method for ‘plotMDS’ with signature ‘"DGEList","ANY","ANY","ANY"’: no definition for class “DGEList”
in method for ‘plotMDS’ with signature ‘"SpatialExperiment"’: no definition for class “SpatialExperiment”
in method for ‘plotRLExpr’ with signature ‘"DGEList","ANY"’: no definition for class “DGEList”
** help
*** installing help indices
*** copying figures
** 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 (standR)
nebbiolo1 Summary
[top]
| Package: standR |
| Version: 0.99.9 |
| RVersion: 4.2
|
| BiocVersion: 3.15
|
| BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data standR |
| BuildTime: 2 minutes 2.66 seconds |
| CheckCommand: BiocCheckGitClone('standR') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings standR_0.99.9.tar.gz && BiocCheck('standR_0.99.9.tar.gz', `new-package`=TRUE) |
| CheckTime: 3 minutes 17.16 seconds |
| BuildBinCommand: |
| BuildBinTime: |
| PackageFileSize: 3239.55 KiB |
| BuildID:: standR_20220409102928 |
| PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: standR. 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: 1. |
nebbiolo1 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘standR/DESCRIPTION’ ... OK
* preparing ‘standR’:
* 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 ‘standR_0.99.9.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('standR')
===============================
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/2574/4de64716797d6328047118e13ee365b45dd3c070/standR.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 ‘standR/DESCRIPTION’ ... OK
* this is package ‘standR’ version ‘0.99.9’
* 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 ‘standR’ can be installed ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... 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 ... [15s/15s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [16s/16s] ERROR
Running examples in ‘standR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geomxNorm
> ### Title: Perform normalization to GeoMX data
> ### Aliases: geomxNorm
>
> ### ** Examples
>
> data("dkd_spe_subset")
>
> spe_tmm <- geomxNorm(dkd_spe_subset, method = "TMM")
> head(assay(spe_tmm, "logcounts"))
Error in assay(spe_tmm, "logcounts") : could not find function "assay"
Calls: head
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [42s/60s]
[42s/60s] 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: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2574/4de64716797d6328047118e13ee365b45dd3c070/standR.Rcheck/00check.log’
for details.
===============================
BiocCheck('standR_0.99.9.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/2574/4de64716797d6328047118e13ee365b45dd3c070/standR_0.99.9.tar.gz" "/tmp/RtmpHWmj8N/file679521bb35f90/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...
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of standR...
* Checking coding practice...
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/plotGeneQCs.R (line 46, column 10)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 5 functions > 50 lines.
The longest 5 functions are:
geomx_import_fun() (R/geomx_import_data.R, line 38): 109 lines
plotPCAbiplot() (R/pcaOtherPlotting.R, line 170): 74 lines
plotROIQC() (R/plotLibQC.R, line 33): 69 lines
geomxNorm() (R/normalisation.R, line 50): 68 lines
plotPairPCA() (R/pcaOtherPlotting.R, line 30): 65 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; 165 lines (5%) are > 80 characters
long.
First 6 lines:
R/addQCstat.R:4 #' @param sample_fraction Double. Genes with low count ...
R/addQCstat.R:5 #' @param rm_genes Logical. Decide whether genes with l...
R/addQCstat.R:6 #' @param min_count Integer. Minimum read count to calc...
R/addQCstat.R:7 #' @param design Generate using `model.matrix`, if this...
R/addQCstat.R:17 addPerROIQC <- function(spe_object, sample_fraction = ...
R/addQCstat.R:37 ###### Genes with low count in more than the thresho...
* NOTE: Consider multiples of 4 spaces for line indents, 797
lines(23%) are not.
First 6 lines:
R/addQCstat.R:18 spe <- spe_object
R/addQCstat.R:20 stopifnot(nrow(spe) > 0)
R/addQCstat.R:21 stopifnot(ncol(spe) > 0)
R/addQCstat.R:22 stopifnot(length(SummarizedExperiment::assayNames(sp...
R/addQCstat.R:23 stopifnot(sample_fraction <= 1 & sample_fraction >= 0)
R/addQCstat.R:24 stopifnot(min_count >= 0)
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: 4
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]