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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:tRanslatome.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings tRanslatome_1.37.6.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/tRanslatome.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-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 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘tRanslatome/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘tRanslatome’ version ‘1.37.6’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'limma', 'anota', 'DESeq2', 'edgeR', 'RankProd', 'topGO',
  'org.Hs.eg.db', 'GOSemSim', 'Heatplus', 'gplots', 'plotrix',
  'Biobase'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘tRanslatome’ 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
* 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 ... NOTE
methodLimma: no visible global function definition for ‘lmFit’
methodTTest: no visible global function definition for ‘calcTStatFast’
GOEnrichment,DEGs: no visible global function definition for ‘toTable’
Undefined global functions or variables:
  calcTStatFast lmFit toTable
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
GOEnrichment 15.329  0.067  15.429
GOComparison 14.855  0.464  15.332
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘tRanslatome_package.Rnw’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘tRanslatome_package.Rnw’ using Sweave
Loading required package: limma
Loading required package: anota
Loading required package: qvalue
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object is masked from ‘package:limma’:

    plotMA

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, aperm, 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

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

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

Loading required package: Biobase
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

Loading required package: edgeR
Loading required package: RankProd
Loading required package: Rmpfr
Loading required package: gmp

Attaching package: ‘gmp’

The following objects are masked from ‘package:base’:

    %*%, apply, crossprod, matrix, tcrossprod

C code of R package 'Rmpfr': GMP using 64 bits per limb


Attaching package: ‘Rmpfr’

The following object is masked from ‘package:gmp’:

    outer

The following objects are masked from ‘package:SummarizedExperiment’:

    cbind, rbind

The following objects are masked from ‘package:IRanges’:

    cbind, pmax, pmin, rbind

The following objects are masked from ‘package:S4Vectors’:

    cbind, rbind

The following objects are masked from ‘package:BiocGenerics’:

    cbind, pmax, pmin, rbind

The following objects are masked from ‘package:stats’:

    dbinom, dgamma, dnbinom, dnorm, dpois, dt, pnorm

The following objects are masked from ‘package:base’:

    cbind, pmax, pmin, rbind

Loading required package: topGO
Loading required package: graph
Loading required package: GO.db
Loading required package: AnnotationDbi

Loading required package: SparseM

Attaching package: ‘SparseM’

The following object is masked from ‘package:base’:

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: ‘topGO’

The following object is masked from ‘package:IRanges’:

    members

Loading required package: org.Hs.eg.db

Loading required package: GOSemSim
GOSemSim v2.25.0  For help: https://yulab-smu.top/biomedical-knowledge-mining-book/

If you use GOSemSim in published research, please cite:
- Guangchuang Yu. Gene Ontology Semantic Similarity Analysis Using GOSemSim. In: Kidder B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, 2020, 2117:207-215. Humana, New York, NY. doi:10.1007/978-1-0716-0301-7_11
- Guangchuang Yu, Fei Li, Yide Qin, Xiaochen Bo, Yibo Wu, Shengqi Wang. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics 2010, 26(7):976-978. doi:10.1093/bioinformatics/btq064


Loading required package: Heatplus
Loading required package: gplots

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: plotrix

Attaching package: ‘plotrix’

The following object is masked from ‘package:gplots’:

    plotCI


Building most specific GOs .....
	( 1836 GO terms found. )

Build GO DAG topology ..........
	( 2024 GO terms and 3404 relations. )

Annotating nodes ...............
	( 19869 genes annotated to the GO terms. )

			 -- Elim Algorithm -- 

		 the algorithm is scoring 178 nontrivial nodes
		 parameters: 
			 test statistic: fisher
			 cutOff: 0.01

	 Level 11:	3 nodes to be scored	(0 eliminated genes)

	 Level 10:	7 nodes to be scored	(0 eliminated genes)

	 Level 9:	13 nodes to be scored	(0 eliminated genes)

	 Level 8:	20 nodes to be scored	(23 eliminated genes)

	 Level 7:	30 nodes to be scored	(23 eliminated genes)

	 Level 6:	34 nodes to be scored	(3034 eliminated genes)

	 Level 5:	27 nodes to be scored	(3336 eliminated genes)

	 Level 4:	21 nodes to be scored	(7623 eliminated genes)

	 Level 3:	20 nodes to be scored	(7623 eliminated genes)

	 Level 2:	2 nodes to be scored	(7623 eliminated genes)

	 Level 1:	1 nodes to be scored	(7623 eliminated genes)

Building most specific GOs .....
	( 1836 GO terms found. )

Build GO DAG topology ..........
	( 2024 GO terms and 3404 relations. )

Annotating nodes ...............
	( 19869 genes annotated to the GO terms. )

			 -- Elim Algorithm -- 

		 the algorithm is scoring 181 nontrivial nodes
		 parameters: 
			 test statistic: fisher
			 cutOff: 0.01

	 Level 12:	1 nodes to be scored	(0 eliminated genes)

	 Level 11:	6 nodes to be scored	(0 eliminated genes)

	 Level 10:	11 nodes to be scored	(62 eliminated genes)

	 Level 9:	12 nodes to be scored	(62 eliminated genes)

	 Level 8:	23 nodes to be scored	(474 eliminated genes)

	 Level 7:	28 nodes to be scored	(523 eliminated genes)

	 Level 6:	29 nodes to be scored	(3040 eliminated genes)

	 Level 5:	25 nodes to be scored	(3295 eliminated genes)

	 Level 4:	23 nodes to be scored	(7500 eliminated genes)

	 Level 3:	20 nodes to be scored	(7500 eliminated genes)

	 Level 2:	2 nodes to be scored	(7500 eliminated genes)

	 Level 1:	1 nodes to be scored	(7500 eliminated genes)
preparing gene to GO mapping data...
Killed

* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/tRanslatome.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL tRanslatome
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’
* installing *source* package ‘tRanslatome’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package can be loaded from final location

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
** testing if installed package keeps a record of temporary installation path
* DONE (tRanslatome)