lconway Summary
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Package: dar |
Version: 0.99.0 |
RVersion: 4.3
|
BiocVersion: 3.18
|
BuildCommand: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data dar |
BuildTime: 4 minutes 41.88 seconds |
CheckCommand: BiocCheckGitClone('dar') && /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --library=/Users/pkgbuild/packagebuilder/workers/jobs/3158/R-libs --install=check:/Users/pkgbuild/packagebuilder/workers/jobs/3158/dar_20230921142858/dar.install-out.txt dar_0.99.0.tar.gz && BiocCheck('dar_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 7 minutes 28.91 seconds |
BuildBinCommand: /Users/biocbuild/BBS/utils/build-universal.sh dar_0.99.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R libdir |
BuildBinTime: 0 minutes 15.55 seconds |
PackageFileSize: 1879.72 KiB |
BuildID:: dar_20230921142858 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: dar. Starting Build package. Starting Check package. Starting Build package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.Checking Package status: 0. Build Package status: 0. |
lconway BUILD SRC output
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===============================
R CMD BUILD
===============================
* checking for file ‘dar/DESCRIPTION’ ... OK
* preparing ‘dar’:
* 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
WARNING: directory ‘dar/dev’ is empty
* looking to see if a ‘data/datalist’ file should be added
* building ‘dar_0.99.0.tar.gz’
lconway CHECK output
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===============================
BiocCheckGitClone('dar')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: dar
─ PackageVersion: 0.99.0
─ sourceDir: /Users/pkgbuild/packagebuilder/workers/jobs/3158/dar_20230921142858/dar
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/3158/dar_20230921142858/dar.Rcheck’
* using R version 4.3.1 Patched (2023-06-17 r84564)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dar/DESCRIPTION’ ... OK
* this is package ‘dar’ 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 ‘dar’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [4s/4s] 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/16s] NOTE
.abundance_boxplot: no visible binding for global variable
‘method_count’
.abundance_boxplot: no visible binding for global variable ‘taxa’
.abundance_boxplot: no visible binding for global variable ‘value’
.abundance_heatmap: no visible binding for global variable
‘method_count’
.abundance_heatmap: no visible binding for global variable ‘taxa’
.abundance_heatmap: no visible binding for global variable ‘value’
.count_summary: no visible binding for global variable ‘value’
.otu_method_count: no visible binding for global variable ‘value’
.zero_groups: no visible binding for global variable ‘value’
.zero_groups: no visible binding for global variable ‘no_zero’
.zero_stats: no visible binding for global variable ‘value’
.zero_stats: no visible binding for global variable ‘n_zero’
find_intersections: no visible binding for global variable ‘value’
find_intersections: no visible binding for global variable ‘name’
find_intersections: no visible binding for global variable
‘sum_methods’
kruskal_test: no visible binding for global variable ‘value’
kruskal_test: no visible binding for global variable ‘pvalue’
prepro_lefse : <anonymous>: no visible binding for global variable
‘Kingdom’
prepro_lefse: no visible binding for global variable ‘RTC’
run_aldex : <anonymous> : <anonymous>: no visible binding for global
variable ‘effect’
run_aldex : <anonymous> : <anonymous>: no visible binding for global
variable ‘we.eBH’
run_ancom : <anonymous> : <anonymous>: no visible binding for global
variable ‘value’
run_ancom : <anonymous> : <anonymous>: no visible binding for global
variable ‘otu_id’
run_ancom : <anonymous> : <anonymous>: no visible binding for global
variable ‘taxon’
run_ancom : <anonymous> : <anonymous>: no visible binding for global
variable ‘lfc’
run_bake: no visible binding for global variable ‘method’
run_bake: no visible binding for global variable ‘method_count’
run_bake: no visible binding for global variable ‘ponderation’
run_bake: no visible binding for global variable ‘taxa’
run_corncob : <anonymous> : <anonymous>: no visible binding for global
variable ‘taxa’
run_corncob : <anonymous> : <anonymous>: no visible binding for global
variable ‘padj’
run_deseq : <anonymous> : <anonymous>: no visible binding for global
variable ‘log2FoldChange’
run_deseq : <anonymous> : <anonymous>: no visible binding for global
variable ‘padj’
run_filter_taxa: no visible binding for global variable ‘pct’
run_lefse : <anonymous> : <anonymous>: no visible binding for global
variable ‘Names’
run_lefse : <anonymous> : <anonymous>: no visible binding for global
variable ‘otu’
run_lefse : <anonymous> : <anonymous>: no visible binding for global
variable ‘pvalue’
run_lefse : <anonymous> : <anonymous>: no visible binding for global
variable ‘scores’
run_lefse : <anonymous> : <anonymous>: no visible binding for global
variable ‘adjp’
run_maaslin : <anonymous> : <anonymous>: no visible binding for global
variable ‘metadata’
run_maaslin : <anonymous> : <anonymous>: no visible binding for global
variable ‘value’
run_maaslin : <anonymous> : <anonymous>: no visible binding for global
variable ‘coef’
run_maaslin : <anonymous> : <anonymous>: no visible binding for global
variable ‘feature’
run_maaslin : <anonymous> : <anonymous>: no visible binding for global
variable ‘qval’
run_metagenomeseq : <anonymous> : <anonymous>: no visible binding for
global variable ‘pvalues’
run_metagenomeseq : <anonymous> : <anonymous>: no visible binding for
global variable ‘adjPvalues’
run_metagenomeseq : <anonymous> : <anonymous>: no visible binding for
global variable ‘padj’
run_wilcox : <anonymous>: no visible binding for global variable
‘estimate’
run_wilcox : <anonymous>: no visible binding for global variable ‘padj’
exclusion_plt,prep_recipe: no visible binding for global variable
‘method’
exclusion_plt,prep_recipe: no visible binding for global variable
‘total’
mutual_plt,prep_recipe: no visible binding for global variable
‘method_count’
mutual_plt,prep_recipe: no visible binding for global variable ‘method’
mutual_plt,prep_recipe: no visible binding for global variable
‘comparison’
mutual_plt,prep_recipe: no visible binding for global variable ‘taxa’
mutual_plt,prep_recipe: no visible binding for global variable
‘effect_v’
mutual_plt,prep_recipe: no visible binding for global variable ‘effect’
show,prep_recipe: no visible binding for global variable ‘sum_methods’
zero_otu,phyloseq: no visible binding for global variable ‘value’
zero_otu,phyloseq: no visible binding for global variable ‘no_zero’
zero_otu,phyloseq: no visible binding for global variable ‘total’
zero_otu,phyloseq: no visible binding for global variable ‘pct’
zero_otu,recipe: no visible binding for global variable ‘value’
zero_otu,recipe: no visible binding for global variable ‘no_zero’
zero_otu,recipe: no visible binding for global variable ‘total’
zero_otu,recipe: no visible binding for global variable ‘pct’
Undefined global functions or variables:
Kingdom Names RTC adjPvalues adjp coef comparison effect effect_v
estimate feature lfc log2FoldChange metadata method method_count
n_zero name no_zero otu otu_id padj pct ponderation pvalue pvalues
qval scores sum_methods taxa taxon total value we.eBH
Consider adding
importFrom("stats", "coef")
to your NAMESPACE file.
* 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 ... [4s/4s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [92s/324s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
step_rarefaction 29.111 1.665 31.418
abundance_plt 19.418 0.374 19.798
prep 1.532 0.052 30.411
step_ancom 1.244 0.063 58.704
import_steps 1.106 0.070 23.524
export_steps 1.064 0.106 8.914
step_lefse 1.006 0.046 35.696
step_metagenomeseq 0.627 0.022 14.995
step_aldex 0.624 0.022 16.832
recipe 0.565 0.017 12.290
step_wilcox 0.556 0.020 13.199
step_deseq 0.539 0.018 12.373
step_corncob 0.468 0.014 7.643
step_maaslin 0.461 0.015 7.416
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [7s/7s]
[7s/7s] 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 ... [5s/5s] OK
* DONE
Status: 1 NOTE
See
‘/Users/pkgbuild/packagebuilder/workers/jobs/3158/dar_20230921142858/dar.Rcheck/00check.log’
for details.
===============================
BiocCheck('dar_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: dar
─ PackageVersion: 0.99.0
─ sourceDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXYaoAz/file1424a3eb17bfe/dar
─ installDir: /var/folders/db/d7_0z9ss4n3692ppdmx9hlgr0000gv/T//RtmpXYaoAz/file1424a49c06337
─ BiocCheckDir: /Users/pkgbuild/packagebuilder/workers/jobs/3158/dar_20230921142858/dar.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2.0 to 4.3.0.
* 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 recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Registered S3 methods overwritten by 'vegan':
method from
reorder.hclust seriation
rev.hclust dendextend
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of dar...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 26 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 35 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 2216 lines
(22%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 6 NOTES
See the dar.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
lconway BUILD BIN output
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===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir dar_0.99.0.tar.gz'
>>>>>>>
* installing *source* package ‘dar’ ...
** using staged installation
** R
** data
** 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 (dar)
nebbiolo2 Summary
[top]
Package: dar |
Version: 0.99.0 |
RVersion: 4.3
|
BiocVersion: 3.18
|
BuildCommand: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data dar |
BuildTime: 7 minutes 4.16 seconds |
CheckCommand: BiocCheckGitClone('dar') && /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --no-vignettes --timings --library=/home/pkgbuild/packagebuilder/workers/jobs/3158/R-libs --install=check:/home/pkgbuild/packagebuilder/workers/jobs/3158/dar_20230921142858/dar.install-out.txt dar_0.99.0.tar.gz && BiocCheck('dar_0.99.0.tar.gz', `new-package`=TRUE) |
CheckTime: 11 minutes 10.26 seconds |
BuildBinCommand: |
BuildBinTime: |
PackageFileSize: 1842.29 KiB |
BuildID:: dar_20230921142858 |
PreProcessing: Starting Git clone. Installing dependencies. Checking Git Clone. Installing package: dar. Starting Build package. Starting Check package. |
PostProcessing: Finished Git clone. Package type: Software. Installing dependency status: 0. Checking git clone status: 0. Installing package status: 0. Build Package status: 0. Adding Build Product Information to Database.WARNING: check time exceeded 10 min. |
nebbiolo2 BUILD SRC output
[top]
===============================
R CMD BUILD
===============================
* checking for file ‘dar/DESCRIPTION’ ... OK
* preparing ‘dar’:
* 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
WARNING: directory ‘dar/dev’ is empty
* looking to see if a ‘data/datalist’ file should be added
* building ‘dar_0.99.0.tar.gz’
nebbiolo2 CHECK output
[top]
===============================
BiocCheckGitClone('dar')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: dar
─ PackageVersion: 0.99.0
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3158/dar_20230921142858/dar
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3158/dar_20230921142858/dar.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dar/DESCRIPTION’ ... OK
* this is package ‘dar’ 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 ‘dar’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [21s/21s] NOTE
.abundance_boxplot: no visible binding for global variable
‘method_count’
.abundance_boxplot: no visible binding for global variable ‘taxa’
.abundance_boxplot: no visible binding for global variable ‘value’
.abundance_heatmap: no visible binding for global variable
‘method_count’
.abundance_heatmap: no visible binding for global variable ‘taxa’
.abundance_heatmap: no visible binding for global variable ‘value’
.count_summary: no visible binding for global variable ‘value’
.otu_method_count: no visible binding for global variable ‘value’
.zero_groups: no visible binding for global variable ‘value’
.zero_groups: no visible binding for global variable ‘no_zero’
.zero_stats: no visible binding for global variable ‘value’
.zero_stats: no visible binding for global variable ‘n_zero’
find_intersections: no visible binding for global variable ‘value’
find_intersections: no visible binding for global variable ‘name’
find_intersections: no visible binding for global variable
‘sum_methods’
kruskal_test: no visible binding for global variable ‘value’
kruskal_test: no visible binding for global variable ‘pvalue’
prepro_lefse : <anonymous>: no visible binding for global variable
‘Kingdom’
prepro_lefse: no visible binding for global variable ‘RTC’
run_aldex : <anonymous> : <anonymous>: no visible binding for global
variable ‘effect’
run_aldex : <anonymous> : <anonymous>: no visible binding for global
variable ‘we.eBH’
run_ancom : <anonymous> : <anonymous>: no visible binding for global
variable ‘value’
run_ancom : <anonymous> : <anonymous>: no visible binding for global
variable ‘otu_id’
run_ancom : <anonymous> : <anonymous>: no visible binding for global
variable ‘taxon’
run_ancom : <anonymous> : <anonymous>: no visible binding for global
variable ‘lfc’
run_bake: no visible binding for global variable ‘method’
run_bake: no visible binding for global variable ‘method_count’
run_bake: no visible binding for global variable ‘ponderation’
run_bake: no visible binding for global variable ‘taxa’
run_corncob : <anonymous> : <anonymous>: no visible binding for global
variable ‘taxa’
run_corncob : <anonymous> : <anonymous>: no visible binding for global
variable ‘padj’
run_deseq : <anonymous> : <anonymous>: no visible binding for global
variable ‘log2FoldChange’
run_deseq : <anonymous> : <anonymous>: no visible binding for global
variable ‘padj’
run_filter_taxa: no visible binding for global variable ‘pct’
run_lefse : <anonymous> : <anonymous>: no visible binding for global
variable ‘Names’
run_lefse : <anonymous> : <anonymous>: no visible binding for global
variable ‘otu’
run_lefse : <anonymous> : <anonymous>: no visible binding for global
variable ‘pvalue’
run_lefse : <anonymous> : <anonymous>: no visible binding for global
variable ‘scores’
run_lefse : <anonymous> : <anonymous>: no visible binding for global
variable ‘adjp’
run_maaslin : <anonymous> : <anonymous>: no visible binding for global
variable ‘metadata’
run_maaslin : <anonymous> : <anonymous>: no visible binding for global
variable ‘value’
run_maaslin : <anonymous> : <anonymous>: no visible binding for global
variable ‘coef’
run_maaslin : <anonymous> : <anonymous>: no visible binding for global
variable ‘feature’
run_maaslin : <anonymous> : <anonymous>: no visible binding for global
variable ‘qval’
run_metagenomeseq : <anonymous> : <anonymous>: no visible binding for
global variable ‘pvalues’
run_metagenomeseq : <anonymous> : <anonymous>: no visible binding for
global variable ‘adjPvalues’
run_metagenomeseq : <anonymous> : <anonymous>: no visible binding for
global variable ‘padj’
run_wilcox : <anonymous>: no visible binding for global variable
‘estimate’
run_wilcox : <anonymous>: no visible binding for global variable ‘padj’
exclusion_plt,prep_recipe: no visible binding for global variable
‘method’
exclusion_plt,prep_recipe: no visible binding for global variable
‘total’
mutual_plt,prep_recipe: no visible binding for global variable
‘method_count’
mutual_plt,prep_recipe: no visible binding for global variable ‘method’
mutual_plt,prep_recipe: no visible binding for global variable
‘comparison’
mutual_plt,prep_recipe: no visible binding for global variable ‘taxa’
mutual_plt,prep_recipe: no visible binding for global variable
‘effect_v’
mutual_plt,prep_recipe: no visible binding for global variable ‘effect’
show,prep_recipe: no visible binding for global variable ‘sum_methods’
zero_otu,phyloseq: no visible binding for global variable ‘value’
zero_otu,phyloseq: no visible binding for global variable ‘no_zero’
zero_otu,phyloseq: no visible binding for global variable ‘total’
zero_otu,phyloseq: no visible binding for global variable ‘pct’
zero_otu,recipe: no visible binding for global variable ‘value’
zero_otu,recipe: no visible binding for global variable ‘no_zero’
zero_otu,recipe: no visible binding for global variable ‘total’
zero_otu,recipe: no visible binding for global variable ‘pct’
Undefined global functions or variables:
Kingdom Names RTC adjPvalues adjp coef comparison effect effect_v
estimate feature lfc log2FoldChange metadata method method_count
n_zero name no_zero otu otu_id padj pct ponderation pvalue pvalues
qval scores sum_methods taxa taxon total value we.eBH
Consider adding
importFrom("stats", "coef")
to your NAMESPACE file.
* 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 ... [6s/6s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [149s/506s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
step_rarefaction 42.628 2.003 44.956
abundance_plt 28.796 0.436 29.236
step_ancom 5.753 0.384 95.532
step_lefse 4.400 0.292 67.186
prep 3.393 0.274 44.489
import_steps 2.192 0.165 31.558
step_metagenomeseq 1.697 0.115 25.560
export_steps 1.634 0.111 11.982
step_aldex 1.613 0.113 22.723
step_deseq 1.629 0.084 21.618
step_wilcox 1.349 0.083 21.570
step_corncob 1.145 0.052 13.768
recipe 1.130 0.041 17.606
step_maaslin 0.964 0.027 11.725
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [11s/11s]
[11s/11s] 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 ... [3s/4s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3158/dar_20230921142858/dar.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('dar_0.99.0.tar.gz')
===============================
─ BiocCheckVersion: 1.37.16
─ BiocVersion: 3.18
─ Package: dar
─ PackageVersion: 0.99.0
─ sourceDir: /tmp/Rtmp9gfaDJ/file1b54b31a0c290/dar
─ installDir: /tmp/Rtmp9gfaDJ/file1b54b35f630fa2
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3158/dar_20230921142858/dar.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2.0 to 4.3.0.
* 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 recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
Registered S3 methods overwritten by 'vegan':
method from
reorder.hclust seriation
rev.hclust dendextend
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of dar...
* Checking coding practice...
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 26 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 35 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 2216 lines
(22%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 6 NOTES
See the dar.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
nebbiolo2 BUILD BIN output
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