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BiocCheckGitClone('LipidSigR')
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─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: LipidSigR
─ PackageVersion: 0.99.22
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2631/b140d49c42f3183d5b79994f52899001935fc4cc/LipidSigR
─ 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
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2631/b140d49c42f3183d5b79994f52899001935fc4cc/LipidSigR.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘LipidSigR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘LipidSigR’ version ‘0.99.22’
* 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 ‘LipidSigR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [11s/11s] 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 ... WARNING
Data codoc mismatches from documentation object 'DE_exp_data':
Variables in data frame 'DE_exp_data'
Code: control_01 control_02 control_03 control_04 control_05
control_06 control_07 control_08 control_09 control_10 feature
hfref_patient_01 hfref_patient_02 hfref_patient_03
hfref_patient_04 hfref_patient_05 hfref_patient_06
hfref_patient_07 hfref_patient_08 hfref_patient_09
hfref_patient_10 hfref_patient_11 hfref_patient_12
hfref_patient_13
Docs: - - control_01 control_10 feature hfref_patient_01
hfref_patient_13
Data codoc mismatches from documentation object 'corr_exp_data':
Variables in data frame 'corr_exp_data'
Code: feature sample1 sample10 sample100 sample101 sample102
sample103 sample104 sample105 sample106 sample107 sample108
sample109 sample11 sample110 sample111 sample112 sample113
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sample90 sample91 sample92 sample93 sample94 sample95 sample96
sample97 sample98 sample99
Docs: - feature sample1 sample129
Data codoc mismatches from documentation object 'profiling_exp_data':
Variables in data frame 'profiling_exp_data'
Code: control_01 control_02 control_03 control_04 control_05
control_06 control_07 control_08 control_09 control_10 feature
hfref_patient_01 hfref_patient_02 hfref_patient_03
hfref_patient_04 hfref_patient_05 hfref_patient_06
hfref_patient_07 hfref_patient_08 hfref_patient_09
hfref_patient_10 hfref_patient_11 hfref_patient_12
hfref_patient_13
Docs: - - control_01 control_10 feature hfref_patient_01
hfref_patient_13
* 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 ... [0s/0s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] ERROR
Running examples in ‘LipidSigR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ML_final
> ### Title: ML_final
> ### Aliases: ML_final
>
> ### ** Examples
>
> library(dplyr)
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
> data("ML_exp_data")
> data("ML_lipid_char_table")
> data("ML_condition_table")
> lipid_char_table <- ML_lipid_char_table[1:40, ]
> condition_table <- ML_condition_table[85:144, ]
> exp_data <- ML_exp_data[1:40, ] %>%
+ select(feature, condition_table$sample_name)
> char_var <- colnames(lipid_char_table)[-1]
> ML_data <- ML_data_process(exp_data, group_info = condition_table,
+ lipid_char_table, char_var[1],
+ exclude_var_missing=TRUE, missing_pct_limit=50,
+ replace_zero=TRUE, zero2what='min', xmin=0.5,
+ replace_NA=TRUE, NA2what='min', ymin=0.5,
+ pct_transform=TRUE, data_transform=TRUE,
+ trans_type='log', centering=FALSE,
+ scaling=FALSE)
> ML_final(ML_data[[2]],ranking_method='Random_forest',
+ ML_method='Random_forest', split_prop=0.3, nfold=3)
[1] "CV fold 1 done"
Error in loadNamespace(x) : there is no package called ‘ranger’
Calls: ML_final ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [66s/70s]
[66s/70s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
2. │ └─LipidSigR (local) ML(ML_data, ranking_method, ML_method, split_prop = split_prop)
3. │ └─LipidSigR (local) feature_selection(train_data, ranking_method, sele_feature_num[b])
4. └─base::loadNamespace(x)
5. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. └─base (local) withOneRestart(expr, restarts[[1L]])
7. └─base (local) doWithOneRestart(return(expr), restart)
── Error ('test-probability_plot.R:16:3'): feature_plot funtcion works ─────────
<packageNotFoundError/error/condition>
Error in `loadNamespace(x)`: there is no package called 'ranger'
Backtrace:
▆
1. ├─LipidSigR::ML_final(...) at test-probability_plot.R:16:2
2. │ └─LipidSigR (local) ML(ML_data, ranking_method, ML_method, split_prop = split_prop)
3. │ └─LipidSigR (local) feature_selection(train_data, ranking_method, sele_feature_num[b])
4. └─base::loadNamespace(x)
5. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
6. └─base (local) withOneRestart(expr, restarts[[1L]])
7. └─base (local) doWithOneRestart(return(expr), restart)
[ FAIL 8 | WARN 194 | SKIP 1 | PASS 219 ]
Error: Test failures
Execution halted
* 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 ... [4s/4s] OK
* DONE
Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2631/b140d49c42f3183d5b79994f52899001935fc4cc/LipidSigR.Rcheck/00check.log’
for details.
===============================
BiocCheck('LipidSigR_0.99.22.tar.gz')
===============================
─ BiocCheckVersion: 1.35.17
─ BiocVersion: 3.17
─ Package: LipidSigR
─ PackageVersion: 0.99.22
─ sourceDir: /tmp/RtmpxIzlNs/file99d214b646f1/LipidSigR
─ installDir: /tmp/RtmpxIzlNs/file99d215c3ef148
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2631/b140d49c42f3183d5b79994f52899001935fc4cc/LipidSigR.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 4.0.0 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 pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 LipidSigR...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 35 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* 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; 50 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 5277 lines
(33%) 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 | 1 WARNINGS | 4 NOTES
See the LipidSigR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.