Ted Natoli
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/cmapR |
| git_branch: master |
| git_last_commit: 42b748a |
| git_last_commit_date: 2021-10-26 12:58:05 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:13 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the cmapR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cmapR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 344/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| cmapR 1.7.0 (landing page) Ted Natoli
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: cmapR |
| Version: 1.7.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cmapR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cmapR_1.7.0.tar.gz |
| StartedAt: 2022-03-17 18:45:12 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:47:34 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 142.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: cmapR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:cmapR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings cmapR_1.7.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/cmapR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cmapR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cmapR' version '1.7.0'
* 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 ... NOTE
Found the following hidden files and directories:
.dockerignore
docs/build/html/.buildinfo
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'cmapR' can be installed ... OK
* checking installed package size ... NOTE
installed size is 5.4Mb
sub-directories of 1Mb or more:
data 2.3Mb
extdata 2.1Mb
* checking package directory ... 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
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: 2 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/cmapR.Rcheck/00check.log'
for details.
cmapR.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL cmapR
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'cmapR' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'cmapR'
finding HTML links ... done
GCT-class html
GCT html
align_matrices html
annotate_gct html
append_dim html
cdesc_char html
check_colnames html
check_dups html
distil html
ds html
extract_gct html
fix_datatypes html
gene_set html
ids html
is.wholenumber html
kd_gct html
lxb2mat html
mat html
melt_gct html
finding level-2 HTML links ... done
merge_gct html
merge_with_precedence html
meta html
na_pad_matrix html
parse_gctx html
parse_gmt html
parse_gmx html
parse_grp html
process_ids html
rank_gct html
read_gctx_ids html
read_gctx_meta html
robust_zscore html
subset_gct html
subset_to_ids html
threshold html
transpose_gct html
update_gctx html
write_gct html
write_gctx html
write_gctx_meta html
write_gmt html
write_grp html
write_tbl html
** 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 (cmapR)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'CompoundDb' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'SpatialExperiment' is missing or broken
done
cmapR.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(cmapR)
>
> test_check("cmapR")
Saving file to foo.gct
Dimensions of matrix: [10x5]
Setting precision to 4
Saved.
Saving file to foo.gct
Dimensions of matrix: [10x5]
Setting precision to 4
Saved.
Saving file to foo.gct
Dimensions of matrix: [10x5]
Setting precision to 4
Saved.
Saving file to ./foo_n272x978.gct
Dimensions of matrix: [978x272]
Setting precision to 4
Saved.
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 168 ]
== Skipped tests ===============================================================
* empty test (2)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 168 ]
>
> proc.time()
user system elapsed
9.95 1.28 11.50
cmapR.Rcheck/cmapR-Ex.timings
| name | user | system | elapsed | |
| GCT | 0.59 | 0.00 | 0.60 | |
| align_matrices | 0 | 0 | 0 | |
| annotate_gct | 0.09 | 0.01 | 0.11 | |
| append_dim | 0 | 0 | 0 | |
| check_colnames | 0 | 0 | 0 | |
| check_dups | 0 | 0 | 0 | |
| distil | 0 | 0 | 0 | |
| extract_gct | 0.06 | 0.02 | 0.07 | |
| fix_datatypes | 0.02 | 0.00 | 0.02 | |
| ids | 0.03 | 0.00 | 0.03 | |
| is.wholenumber | 0 | 0 | 0 | |
| lxb2mat | 0.08 | 0.08 | 0.16 | |
| mat | 0 | 0 | 0 | |
| melt_gct | 1.82 | 0.15 | 1.94 | |
| merge_gct | 0.21 | 0.00 | 0.20 | |
| merge_with_precedence | 0 | 0 | 0 | |
| meta | 0.01 | 0.00 | 0.01 | |
| na_pad_matrix | 0 | 0 | 0 | |
| parse_gctx | 0.18 | 0.02 | 0.19 | |
| parse_gmt | 0.01 | 0.01 | 0.03 | |
| parse_gmx | 0.02 | 0.00 | 0.02 | |
| parse_grp | 0 | 0 | 0 | |
| process_ids | 0.01 | 0.00 | 0.01 | |
| rank_gct | 0.11 | 0.00 | 0.11 | |
| read_gctx_ids | 0 | 0 | 0 | |
| read_gctx_meta | 0.60 | 0.04 | 0.63 | |
| robust_zscore | 0 | 0 | 0 | |
| subset_gct | 0.03 | 0.00 | 0.03 | |
| threshold | 0 | 0 | 0 | |
| transpose_gct | 0.07 | 0.00 | 0.08 | |
| update_gctx | 0 | 0 | 0 | |
| write_gct | 1.08 | 0.12 | 1.20 | |
| write_gctx | 0.25 | 0.08 | 0.92 | |
| write_gctx_meta | 0 | 0 | 0 | |
| write_gmt | 0 | 0 | 0 | |
| write_grp | 0 | 0 | 0 | |
| write_tbl | 0 | 0 | 0 | |