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BUILD report for tidybulk on machv2

This page was generated on 2020-10-17 11:59:47 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE tidybulk PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1797/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tidybulk 1.0.2
Stefano Mangiola
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/tidybulk
Branch: RELEASE_3_11
Last Commit: bfa4dd1
Last Changed Date: 2020-06-08 00:40:18 -0400 (Mon, 08 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK [ OK ] WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: tidybulk
Version: 1.0.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data tidybulk
StartedAt: 2020-10-16 21:35:05 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 21:39:24 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 259.0 seconds
RetCode: 0
Status:  OK 
PackageFile: tidybulk_1.0.2.tar.gz
PackageFileSize: 3.408 MiB

Command output

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###
### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data tidybulk
###
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* checking for file ‘tidybulk/DESCRIPTION’ ... OK
* preparing ‘tidybulk’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* building the PDF package manual
Hmm ... looks like a package
Converting Rd files to LaTeX .........
Creating pdf output from LaTeX ...

This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex)
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entering extended mode
LaTeX2e <2020-02-02> patch level 5
L3 programming layer <2020-02-25>
(./Rd2.tex (/usr/local/texlive/2019/texmf-dist/tex/latex/base/book.cls
Document Class: book 2019/12/20 v1.4l Standard LaTeX document class
(/usr/local/texlive/2019/texmf-dist/tex/latex/base/bk10.clo))
(/Library/Frameworks/R.framework/Resources/share/texmf/tex/latex/Rd.sty
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[]\T1/ptm/m/n/10 <[`tidy-eval`][dplyr_tidy_eval]> Vari-ables, or func-tions or 
vari-ables. Use [desc()]
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 []\T1/zi4/m/n/9 as_matrix(head(dplyr::select(tidybulk::counts_mini, transcript
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 []    \T1/zi4/m/n/9 cluster_elements(tidybulk::counts_mini, sample, transcript
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[]\T1/ptm/m/n/10 impute_abundance() takes as im-put a `tbl` for-mat-ted as | <S
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[]\T1/ptm/m/n/10 reduce_dimensions() takes as im-put a `tbl` for-mat-ted as | <
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 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 

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 []\T1/zi4/m/n/9 counts.PCA =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="PCA", .dims = 3)[] 
[36]
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[]\T1/ptm/m/n/10 remove_redundancy() takes as im-put a `tbl` for-mat-ted as | <
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\T1/ptm/m/n/10 | <...> | for cor-re-la-tion method or | <DI-MEN-SION 1> | <DI-M
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 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
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[40] [41] [42] [43]
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 []\T1/zi4/m/n/9 counts.MDS =  reduce_dimensions(tidybulk::counts_mini, sample,
 transcript, count, method="MDS", .dims = 3)[] 

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 []\T1/zi4/m/n/9 counts.MDS.rotated =  rotate_dimensions(counts.MDS, \TS1/cmtt/
m/n/9 `\T1/zi4/m/n/9 Dim1\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , \TS1/cmtt/m/n/9 `\T1/
zi4/m/n/9 Dim2\TS1/cmtt/m/n/9 `\T1/zi4/m/n/9 , rotation_degrees = 45, .element 
= sample)[] 
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[]\T1/ptm/m/n/10 A string char-ac-ter. Ei-ther "edgeR_quasi_likelihood" (i.e., 
QLF), "edgeR_likelihood_ratio"
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 []\T1/zi4/m/n/9 df_entrez = symbol_to_entrez(tidybulk::counts_mini, .transcrip
t = transcript, .sample = sample)[] 

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 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] 
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 []\T1/zi4/m/n/9 df_entrez = symbol_to_entrez(tidybulk::counts_mini, .transcrip
t = transcript, .sample = sample)[] 

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 []\T1/zi4/m/n/9 df_entrez = aggregate_duplicates(df_entrez, aggregation_functi
on = sum, .sample = sample, .transcript = entrez, .abundance = count)[] 

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 []\T1/zi4/m/n/9 df_entrez = mutate(df_entrez, do_test = transcript %in% c("TNF
RSF4", "PLCH2", "PADI4", "PAX7"))[] 
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[]\T1/ptm/m/n/10 tidybulk() cre-ates a `tt` ob-ject from a `tbl` for-mat-ted as
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(see the transcript file for additional information){/usr/local/texlive/2019/te
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Output written on Rd2.pdf (60 pages, 184367 bytes).
Transcript written on Rd2.log.
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Saving output to ‘/private/tmp/RtmphVvrmj/Rbuild181c17e0b6f86/tidybulk/build/tidybulk.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘tidybulk_1.0.2.tar.gz’