merida1 Summary
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Package: spaSim |
Version: 0.99.0 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data spaSim |
BuildTime: 2 minutes 5.60 seconds |
CheckCommand: BiocCheckGitClone('spaSim') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch spaSim_0.99.0.tar.gz && BiocCheck('spaSim_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 5 minutes 40.98 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh spaSim_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 22.62 seconds |
PackageFileSize: 2380.41 KiB |
BuildID:: spaSim_20220405143953 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: spaSim. 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: 0. Build Package status: 0. |
merida1 BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘spaSim/DESCRIPTION’ ... OK
* preparing ‘spaSim’:
* 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
* building ‘spaSim_0.99.0.tar.gz’
merida1 CHECK output
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===============================
BiocCheckGitClone('spaSim')
===============================
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/2605/spaSim_20220405143953/spaSim.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 ‘spaSim/DESCRIPTION’ ... OK
* this is package ‘spaSim’ version ‘0.99.0’
* 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 ‘spaSim’ can be installed ... [22s/22s] 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 ... [24s/24s] 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [115s/115s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
multiple_images_with_immune_rings 73.029 2.951 76.019
simulate_background_cells 7.753 0.017 7.771
multiple_images_with_clusters 6.556 0.365 6.928
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [47s/47s]
[47s/47s] 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: OK
===============================
BiocCheck('spaSim_0.99.0.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/2605/spaSim_20220405143953/spaSim_0.99.0.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpNMTMtT/file29222ac595ec/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...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.1.0 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...
* 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 spaSim...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/format_sce.R (line 15, column 5)
print() in R/multiple_background_images.R (line 71, column 5)
print() in R/plot_cells.R (line 55, column 7)
print() in R/plot_cells.R (line 101, column 3)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/simulate_double_rings.R (line 132, column 20)
R/simulate_double_rings.R (line 134, column 29)
R/simulate_double_rings.R (line 135, column 35)
R/simulate_immune_rings.R (line 115, column 20)
R/simulate_immune_rings.R (line 116, column 16)
R/simulate_immune_rings.R (line 117, column 29)
R/simulate_immune_rings.R (line 118, column 35)
R/simulate_stripes.R (line 91, column 15)
R/simulate_stripes.R (line 92, column 22)
R/simulate_stripes.R (line 93, column 18)
R/simulate_stripes.R (line 94, column 24)
R/simulate_stripes.R (line 95, column 30)
R/TIS.R (line 105, column 11)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 9 functions > 50 lines.
The longest 5 functions are:
simulate_double_rings() (R/simulate_double_rings.R, line 58):
186 lines
simulate_immune_rings() (R/simulate_immune_rings.R, line 48):
151 lines
simulate_clusters() (R/simulate_clusters.R, line 41): 131 lines
TIS() (R/TIS.R, line 66): 95 lines
multiple_images_with_immune_rings()
(R/multiple_images_with_immune_rings.R, line 58): 93 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; 214 lines (7%) are > 80 characters
long.
First 6 lines:
R/multiple_background_images.R:57 plot_colours <- c("gray","darkg...
R/multiple_background_images.R:99 plot_cells(bg_sample, idents, p...
R/multiple_images_with_clusters.R:79 # if the cluster size is too s...
R/multiple_images_with_clusters.R:86 # if the cluster size is too s...
R/multiple_images_with_clusters.R:98 # if the cluster size is too s...
R/multiple_images_with_clusters.R:114 properties_of_clusters[...
* NOTE: Consider multiples of 4 spaces for line indents, 903
lines(28%) are not.
First 6 lines:
R/format_sce.R:15 #CHECK
R/format_sce.R:16 if (dim(data)[1]==0){
R/format_sce.R:19 }
R/format_sce.R:21 data[,"pseudo"] <- 0
R/format_sce.R:22 assay_data <- data[,"pseudo"]
R/format_sce.R:23 data[,"pseudo"] <- NULL
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: 7
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 spaSim_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘spaSim’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** 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 (spaSim)
nebbiolo1 Summary
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Package: spaSim |
Version: 0.99.0 |
RVersion: 4.2
|
BiocVersion: 3.15
|
BuildCommand: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data spaSim |
BuildTime: 1 minutes 15.78 seconds |
CheckCommand: BiocCheckGitClone('spaSim') && /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --no-vignettes --timings spaSim_0.99.0.tar.gz && BiocCheck('spaSim_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 3 minutes 40.29 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 2387.59 KiB |
BuildID:: spaSim_20220405143953 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: spaSim. 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 ‘spaSim/DESCRIPTION’ ... OK
* preparing ‘spaSim’:
* 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
* building ‘spaSim_0.99.0.tar.gz’
nebbiolo1 CHECK output
[top]
===============================
BiocCheckGitClone('spaSim')
===============================
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/2605/spaSim_20220405143953/spaSim.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 ‘spaSim/DESCRIPTION’ ... OK
* this is package ‘spaSim’ version ‘0.99.0’
* 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 ‘spaSim’ can be installed ... [17s/17s] 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 ... [17s/17s] 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [63s/63s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
multiple_images_with_immune_rings 39.458 0.352 39.811
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [26s/26s]
[26s/26s] 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: OK
===============================
BiocCheck('spaSim_0.99.0.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/2605/spaSim_20220405143953/spaSim_0.99.0.tar.gz" "/tmp/RtmpHzpawT/file1324822e4dcbb4/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...
* NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or
removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R Version dependency...
* NOTE: Update R version dependency from 4.1.0 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...
* 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 spaSim...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/format_sce.R (line 15, column 5)
print() in R/multiple_background_images.R (line 71, column 5)
print() in R/plot_cells.R (line 55, column 7)
print() in R/plot_cells.R (line 101, column 3)
* NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/simulate_double_rings.R (line 132, column 20)
R/simulate_double_rings.R (line 134, column 29)
R/simulate_double_rings.R (line 135, column 35)
R/simulate_immune_rings.R (line 115, column 20)
R/simulate_immune_rings.R (line 116, column 16)
R/simulate_immune_rings.R (line 117, column 29)
R/simulate_immune_rings.R (line 118, column 35)
R/simulate_stripes.R (line 91, column 15)
R/simulate_stripes.R (line 92, column 22)
R/simulate_stripes.R (line 93, column 18)
R/simulate_stripes.R (line 94, column 24)
R/simulate_stripes.R (line 95, column 30)
R/TIS.R (line 105, column 11)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 9 functions > 50 lines.
The longest 5 functions are:
simulate_double_rings() (R/simulate_double_rings.R, line 58):
186 lines
simulate_immune_rings() (R/simulate_immune_rings.R, line 48):
151 lines
simulate_clusters() (R/simulate_clusters.R, line 41): 131 lines
TIS() (R/TIS.R, line 66): 95 lines
multiple_images_with_immune_rings()
(R/multiple_images_with_immune_rings.R, line 58): 93 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; 214 lines (7%) are > 80 characters
long.
First 6 lines:
R/multiple_background_images.R:57 plot_colours <- c("gray","darkg...
R/multiple_background_images.R:99 plot_cells(bg_sample, idents, p...
R/multiple_images_with_clusters.R:79 # if the cluster size is too s...
R/multiple_images_with_clusters.R:86 # if the cluster size is too s...
R/multiple_images_with_clusters.R:98 # if the cluster size is too s...
R/multiple_images_with_clusters.R:114 properties_of_clusters[...
* NOTE: Consider multiples of 4 spaces for line indents, 903
lines(28%) are not.
First 6 lines:
R/format_sce.R:15 #CHECK
R/format_sce.R:16 if (dim(data)[1]==0){
R/format_sce.R:19 }
R/format_sce.R:21 data[,"pseudo"] <- 0
R/format_sce.R:22 assay_data <- data[,"pseudo"]
R/format_sce.R:23 data[,"pseudo"] <- NULL
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: 7
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]