| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:06:52 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 metaseqR2 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metaseqR2.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1106/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| metaseqR2 1.6.1 (landing page) Panagiotis Moulos
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: metaseqR2 |
| Version: 1.6.1 |
| Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaseqR2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings metaseqR2_1.6.1.tar.gz |
| StartedAt: 2022-04-12 22:33:31 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 22:46:13 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 762.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: metaseqR2.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:metaseqR2.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings metaseqR2_1.6.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/metaseqR2.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'metaseqR2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'metaseqR2' version '1.6.1'
* 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 whether package 'metaseqR2' can be installed ... OK
* checking installed package size ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/metaseqR2/libs/i386/metaseqR2.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/metaseqR2/libs/x64/metaseqR2.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getAnnotation 8.92 0.19 12.61
metaseqr2 6.58 2.09 14.91
read2count 8.11 0.01 11.41
statNoiseq 7.39 0.02 7.41
statDeseq2 5.88 0.52 6.40
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
metaseqr2 7.04 1.54 12.16
statNoiseq 7.48 0.00 7.48
getAnnotation 5.85 0.03 10.79
statDeseq2 5.83 0.02 5.84
read2count 5.67 0.05 9.09
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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: 1 NOTE
See
'C:/Users/biocbuild/bbs-3.14-bioc/meat/metaseqR2.Rcheck/00check.log'
for details.
metaseqR2.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/metaseqR2_1.6.1.tar.gz && rm -rf metaseqR2.buildbin-libdir && mkdir metaseqR2.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=metaseqR2.buildbin-libdir metaseqR2_1.6.1.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL metaseqR2_1.6.1.zip && rm metaseqR2_1.6.1.tar.gz metaseqR2_1.6.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
52 2115k 52 1105k 0 0 1414k 0 0:00:01 --:--:-- 0:00:01 1414k
100 2115k 100 2115k 0 0 1719k 0 0:00:01 0:00:01 --:--:-- 1720k
install for i386
* installing *source* package 'metaseqR2' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pval.c -o pval.o
pval.c: In function 'add_from_both_sides':
pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable]
double esttotalperlength = total/2;
^~~~~~~~~~~~~~~~~
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o metaseqR2.dll tmp.def pval.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/metaseqR2.buildbin-libdir/00LOCK-metaseqR2/00new/metaseqR2/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'metaseqR2'
finding HTML links ... done
buildAnnotationDatabase html
buildCustomAnnotation html
combineBonferroni html
combineHarmonic html
combineMaxp html
combineMinp html
combineSimes html
combineWeight html
createSignalTracks html
diagplotAvgFtd html
diagplotBoxplot html
diagplotCor html
diagplotDeHeatmap html
diagplotEdaseq html
diagplotFiltered html
diagplotFtd html
diagplotMds html
diagplotNoiseq html
diagplotPairs html
diagplotRoc html
diagplotVenn html
diagplotVolcano html
downsampleCounts html
estimateAufcWeights html
estimateSimParams html
getAnnotation html
getDefaults html
getInstalledAnnotations html
getWeights html
hg19pvalues html
importCustomAnnotation html
libsizeListMm9 html
loadAnnotation html
makeSimDataSd html
makeSimDataTcc html
metaTest html
metaseqr2 html
finding level-2 HTML links ... done
metaseqrPlot html
mm9GeneCounts html
normalizeAbsseq html
normalizeDeseq html
normalizeDeseq2 html
normalizeDss html
normalizeEdaseq html
normalizeEdger html
normalizeNbpseq html
normalizeNoiseq html
read2count html
readTargets html
sampleListMm9 html
statAbsseq html
statBayseq html
statDeseq html
statDeseq2 html
statDss html
statEdger html
statLimma html
statNbpseq html
statNoiseq 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
install for x64
* installing *source* package 'metaseqR2' ...
** libs
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pval.c -o pval.o
pval.c: In function 'add_from_both_sides':
pval.c:26:11: warning: unused variable 'esttotalperlength' [-Wunused-variable]
double esttotalperlength = total/2;
^~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o metaseqR2.dll tmp.def pval.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/metaseqR2.buildbin-libdir/metaseqR2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'metaseqR2' as metaseqR2_1.6.1.zip
* DONE (metaseqR2)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'metaseqR2' successfully unpacked and MD5 sums checked
|
metaseqR2.Rcheck/tests_i386/runTests.Rout
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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.
> BiocGenerics:::testPackage("metaseqR2")
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Attaching package: 'MatrixGenerics'
The following objects are masked from 'package:matrixStats':
colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
colWeightedMeans, colWeightedMedians, colWeightedSds,
colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
rowWeightedSds, rowWeightedVars
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'Biobase'
The following object is masked from 'package:MatrixGenerics':
rowMedians
The following objects are masked from 'package:matrixStats':
anyMissing, rowMedians
Attaching package: 'limma'
The following object is masked from 'package:DESeq2':
plotMA
The following object is masked from 'package:BiocGenerics':
plotMA
locfit 1.5-9.5 2022-03-01
Attaching package: 'metaseqR2'
The following object is masked from 'package:limma':
readTargets
Downsampling counts...
Estimating initial dispersion population...
Estimating dispersions using log-likelihood...
Running simulations... This procedure requires time... Please wait...Using Ensembl host https://nov2020.archive.ensembl.org
2022-04-12 22:45:02: Data processing started...
Read counts file: imported custom data frame
Conditions: G1, G2
Samples to include: G1_rep1, G1_rep2, G1_rep3, G2_rep1, G2_rep2, G2_rep3
Samples to exclude: none
Requested contrasts: G1_vs_G2
Annotation: embedded
Organism: mm10
Reference source: ensembl
Count type: gene
Analysis preset: all_basic
Transcriptional level: gene
Exon filters: none applied
Gene filters: none applied
Filter application: postnorm
Normalization algorithm: edaseq
Normalization arguments:
within.which: loess
between.which: full
Statistical algorithm(s): edger, limma
Statistical arguments:
edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
limma: none
Meta-analysis method: simes
Multiple testing correction: BH
Logarithmic transformation offset: 1
Analysis preset: all_basic
Quality control plots:
Figure format: png
Output directory: C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpQtg40d
Output data: annotation, p_value, adj_p_value, meta_p_value, adj_meta_p_value, fold_change
Output scale(s): natural, log2
Output values: normalized
Loading gene annotation...
Saving gene model to C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpQtg40d/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edaseq
Running statistical tests with: edger
Contrast: G1_vs_G2
Running statistical tests with: limma
Contrast: G1_vs_G2
Performing meta-analysis with simes
Building output files...
Contrast: G1_vs_G2
Adding non-filtered data...
binding annotation...
binding p-values...
binding FDRs...
binding meta p-values...
binding adjusted meta p-values...
binding natural normalized fold changes...
binding log2 normalized fold changes...
Writing output...
2022-04-12 22:45:03: Data processing finished!
Total processing time: 00 seconds
Estimating AUFC weights... Please wait...
Processing edger
Processing limma
Retrieving edger
Retrieving limma
2022-04-12 22:45:04: Data processing started...
Read counts file: imported custom data frame
Conditions: e14.5, adult_8_weeks
Samples to include: e14.5_1, e14.5_2, a8w_1, a8w_2
Samples to exclude: none
Requested contrasts: adult_8_weeks_vs_e14.5
Library sizes:
e14.5_1: 3102907
e14.5_2: 2067905
a8w_1: 3742059
a8w_2: 4403954
Annotation: embedded
Organism: mm9
Reference source: ensembl
Count type: gene
Analysis preset: medium_basic
Transcriptional level: gene
Exon filters: minActiveExons
minActiveExons:
exonsPerGene: 5
minExons: 2
frac: 0.2
Gene filters: length, avgReads, expression, biotype
length:
length: 500
avgReads:
averagePerBp: 100
quantile: 0.25
expression:
median: TRUE
mean: FALSE
quantile: NA
known: NA
custom: NA
biotype:
pseudogene: FALSE
snRNA: FALSE
protein_coding: FALSE
antisense: FALSE
miRNA: FALSE
lincRNA: FALSE
snoRNA: FALSE
processed_transcript: FALSE
misc_RNA: FALSE
rRNA: TRUE
sense_overlapping: FALSE
sense_intronic: FALSE
polymorphic_pseudogene: FALSE
non_coding: FALSE
three_prime_overlapping_ncrna: FALSE
IG_C_gene: FALSE
IG_J_gene: FALSE
IG_D_gene: FALSE
IG_V_gene: FALSE
ncrna_host: FALSE
Filter application: postnorm
Normalization algorithm: edger
Normalization arguments:
method: TMM
logratioTrim: 0.3
sumTrim: 0.05
doWeighting: TRUE
Acutoff: -1e+10
p: 0.75
Statistical algorithm(s): edger, limma
Statistical arguments:
edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
limma: none
Meta-analysis method: simes
Multiple testing correction: BH
p-value threshold: 0.05
Logarithmic transformation offset: 1
Analysis preset: medium_basic
Quality control plots: mds
Figure format: png
Output directory: C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpQtg40d
Output data: annotation, p_value, adj_p_value, meta_p_value, adj_meta_p_value, fold_change
Output scale(s): natural, log2
Output values: normalized
Loading gene annotation...
Saving gene model to C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpQtg40d/data/gene_model.RData
Removing genes with zero counts in all samples...
Normalizing with: edger
Applying gene filter length...
Threshold below which ignored: 500
Applying gene filter avgReads...
Threshold below which ignored: 0.0659629215631332
Applying gene filter expression...
Threshold below which ignored: 68
Applying gene filter biotype...
Biotypes ignored: rRNA
2106 genes filtered out
1681 genes remain after filtering
Running statistical tests with: edger
Contrast: adult_8_weeks_vs_e14.5
Contrast adult_8_weeks_vs_e14.5: found 906 genes
Running statistical tests with: limma
Contrast: adult_8_weeks_vs_e14.5
Contrast adult_8_weeks_vs_e14.5: found 911 genes
Performing meta-analysis with simes
Building output files...
Contrast: adult_8_weeks_vs_e14.5
Adding non-filtered data...
binding annotation...
binding p-values...
binding FDRs...
binding meta p-values...
binding adjusted meta p-values...
binding natural normalized fold changes...
binding log2 normalized fold changes...
Writing output...
Adding filtered data...
binding annotation...
binding p-values...
binding FDRs...
binding meta p-values...
binding adjusted meta p-values...
binding natural normalized fold changes...
binding log2 normalized fold changes...
Writing output...
Adding report data...
binding annotation...
binding meta p-values...
binding adjusted meta p-values...
binding log2 normalized fold changes...
binding normalized mean counts...
binding normalized mean counts...
Creating quality control graphs...
Plotting in png format...
Plotting mds...
Importing mds...
Writing plot database in C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpQtg40d/data/reportdb.js
Creating HTML report...
Compressing figures... adding: Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpQtg40d/plots/qc/mds.png (deflated 62%)
Downloading required JavaScript libraries...trying URL 'https://raw.github.com/HubSpot/pace/v1.0.0/pace.min.js'
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processing file: metaseqr2_report.Rmd
inline R code fragments
label: knitr_init (with options)
List of 2
$ echo : logi FALSE
$ cache: logi FALSE
ordinary text without R code
label: load_js
ordinary text without R code
label: pace_opts (with options)
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$ engine: chr "js"
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label: decide_dexie
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label: define_getplot_funs (with options)
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label: report_init
Attaching package: 'gplots'
The following object is masked from 'package:IRanges':
space
The following object is masked from 'package:S4Vectors':
space
The following object is masked from 'package:stats':
lowess
Loading required package: plotly
Loading required package: ggplot2
Attaching package: 'plotly'
The following object is masked from 'package:ggplot2':
last_plot
The following object is masked from 'package:IRanges':
slice
The following object is masked from 'package:S4Vectors':
rename
The following object is masked from 'package:stats':
filter
The following object is masked from 'package:graphics':
layout
Loading required package: viridis
Loading required package: viridisLite
======================
Welcome to heatmaply version 1.3.0
Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.
The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
You may ask questions at stackoverflow, use the r and heatmaply tags:
https://stackoverflow.com/questions/tagged/heatmaply
======================
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output file: metaseqr2_report.knit.md
"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc87c79a12ea3.html --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" +RTS -K2048m -RTS --variable "material:true" --variable "lightbox:true" --variable "thumbnails:true" --variable "gallery:true" --variable "cards:true" --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --template "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmdformats\templates\material\material.html" --highlight-style kate --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpQtg40d\rmarkdown-str87c58bb48c9.html"
Output created: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpQtg40d/index.html
2022-04-12 22:45:16: Data processing finished!
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RUNIT TEST PROTOCOL -- Tue Apr 12 22:45:16 2022
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R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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.
> BiocGenerics:::testPackage("metaseqR2")
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Welcome to Bioconductor
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Downsampling counts...
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2022-04-12 22:45:48: Data processing started...
Read counts file: imported custom data frame
Conditions: G1, G2
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Samples to exclude: none
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Reference source: ensembl
Count type: gene
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Output directory: C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpCamXyq
Output data: annotation, p_value, adj_p_value, meta_p_value, adj_meta_p_value, fold_change
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a8w_1: 3742059
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protein_coding: FALSE
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limma: none
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p-value threshold: 0.05
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Analysis preset: medium_basic
Quality control plots: mds
Figure format: png
Output directory: C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpCamXyq
Output data: annotation, p_value, adj_p_value, meta_p_value, adj_meta_p_value, fold_change
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Loading gene annotation...
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Biotypes ignored: rRNA
2106 genes filtered out
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Contrast adult_8_weeks_vs_e14.5: found 906 genes
Running statistical tests with: limma
Contrast: adult_8_weeks_vs_e14.5
Contrast adult_8_weeks_vs_e14.5: found 911 genes
Performing meta-analysis with simes
Building output files...
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binding normalized mean counts...
binding normalized mean counts...
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processing file: metaseqr2_report.Rmd
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======================
Welcome to heatmaply version 1.3.0
Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.
The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
You may ask questions at stackoverflow, use the r and heatmaply tags:
https://stackoverflow.com/questions/tagged/heatmaply
======================
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$ engine: chr "js"
output file: metaseqr2_report.knit.md
"C:/PROGRA~1/Pandoc/pandoc" +RTS -K512m -RTS metaseqr2_report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output pandoc154416c755ed.html --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\pagebreak.lua" --lua-filter "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmarkdown\rmarkdown\lua\latex-div.lua" +RTS -K2048m -RTS --variable "material:true" --variable "lightbox:true" --variable "thumbnails:true" --variable "gallery:true" --variable "cards:true" --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 1 --template "C:\Users\biocbuild\bbs-3.14-bioc\R\library\rmdformats\templates\material\material.html" --highlight-style kate --variable theme=bootstrap --include-in-header "C:\Users\biocbuild\bbs-3.14-bioc\tmpdir\RtmpCamXyq\rmarkdown-str154449d93da4.html"
Output created: C:/Users/biocbuild/bbs-3.14-bioc/tmpdir/RtmpCamXyq/index.html
2022-04-12 22:46:01: Data processing finished!
Total processing time: 12 seconds
RUNIT TEST PROTOCOL -- Tue Apr 12 22:46:01 2022
***********************************************
Number of test functions: 2
Number of errors: 0
Number of failures: 0
1 Test Suite :
metaseqR2 RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2
Number of errors: 0
Number of failures: 0
There were 50 or more warnings (use warnings() to see the first 50)
>
> proc.time()
user system elapsed
34.95 2.71 44.70
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metaseqR2.Rcheck/examples_i386/metaseqR2-Ex.timings
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metaseqR2.Rcheck/examples_x64/metaseqR2-Ex.timings
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