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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ExpressionAtlas.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ExpressionAtlas_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ExpressionAtlas.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ExpressionAtlas/DESCRIPTION’ ... OK
* this is package ‘ExpressionAtlas’ version ‘1.24.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ExpressionAtlas’ 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ExpressionAtlas-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name:  searchAtlasExperiments 
> ### Title: Search for Expression Atlas experiments
> ### Aliases: ' searchAtlasExperiments '
> 
> ### ** Examples
> 
>     
>     # Search for experiments on salt in rice.
>     atlasRes <- searchAtlasExperiments( properties = "salt", species = "rice"  )
Searching for Expression Atlas experiments matching your query ...
Query successful.
Specification mandates value for attribute async
attributes construct error
Couldn't find end of Start Tag script line 18
Opening and ending tag mismatch: meta line 17 and script
Opening and ending tag mismatch: meta line 45 and head
Specification mandates value for attribute data-sticky-container
Opening and ending tag mismatch: img line 59 and a
Opening and ending tag mismatch: a line 59 and h1
Opening and ending tag mismatch: h1 line 59 and div
Opening and ending tag mismatch: input line 68 and div
Opening and ending tag mismatch: input line 67 and fieldset
Opening and ending tag mismatch: div line 66 and form
Opening and ending tag mismatch: fieldset line 65 and div
Opening and ending tag mismatch: form line 64 and div
Opening and ending tag mismatch: div line 63 and header
Opening and ending tag mismatch: img line 111 and a
Opening and ending tag mismatch: a line 110 and span
Opening and ending tag mismatch: span line 109 and div
Opening and ending tag mismatch: div line 108 and script
Opening and ending tag mismatch: input line 126 and fieldset
Opening and ending tag mismatch: input line 130 and fieldset
Opening and ending tag mismatch: input line 129 and form
Opening and ending tag mismatch: input line 136 and form
Opening and ending tag mismatch: form line 135 and div
Opening and ending tag mismatch: fieldset line 128 and div
Opening and ending tag mismatch: input line 126 and section
Opening and ending tag mismatch: fieldset line 125 and div
Specification mandates value for attribute defer
attributes construct error
Couldn't find end of Start Tag script line 154
Opening and ending tag mismatch: footer line 153 and script
Opening and ending tag mismatch: input line 125 and footer
Specification mandates value for attribute defer
attributes construct error
Couldn't find end of Start Tag script line 174
Opening and ending tag mismatch: form line 124 and script
EntityRef: expecting ';'
Opening and ending tag mismatch: div line 118 and body
Opening and ending tag mismatch: div line 117 and html
Premature end of data in tag section line 117
Premature end of data in tag script line 107
Premature end of data in tag div line 55
Premature end of data in tag header line 55
Premature end of data in tag div line 54
Premature end of data in tag div line 53
Premature end of data in tag body line 48
Premature end of data in tag link line 42
Premature end of data in tag link line 41
Premature end of data in tag link line 35
Premature end of data in tag link line 34
Premature end of data in tag meta line 33
Premature end of data in tag meta line 32
Premature end of data in tag link line 31
Premature end of data in tag link line 30
Premature end of data in tag link line 29
Premature end of data in tag link line 28
Premature end of data in tag link line 27
Premature end of data in tag link line 26
Premature end of data in tag link line 25
Premature end of data in tag link line 24
Premature end of data in tag link line 22
Premature end of data in tag meta line 16
Premature end of data in tag meta line 15
Premature end of data in tag meta line 14
Premature end of data in tag meta line 13
Premature end of data in tag meta line 12
Premature end of data in tag meta line 11
Premature end of data in tag meta line 10
Premature end of data in tag meta line 9
Premature end of data in tag meta line 8
Premature end of data in tag meta line 7
Premature end of data in tag meta line 5
Premature end of data in tag meta line 4
Premature end of data in tag head line 3
Premature end of data in tag html line 2
Error: 1: Specification mandates value for attribute async
2: attributes construct error
3: Couldn't find end of Start Tag script line 18
4: Opening and ending tag mismatch: meta line 17 and script
5: Opening and ending tag mismatch: meta line 45 and head
6: Specification mandates value for attribute data-sticky-container
7: Opening and ending tag mismatch: img line 59 and a
8: Opening and ending tag mismatch: a line 59 and h1
9: Opening and ending tag mismatch: h1 line 59 and div
10: Opening and ending tag mismatch: input line 68 and div
11: Opening and ending tag mismatch: input line 67 and fieldset
12: Opening and ending tag mismatch: div line 66 and form
13: Opening and ending tag mismatch: fieldset line 65 and div
14: Opening and ending tag mismatch: form line 64 and div
15: Opening and ending tag mismatch: div line 63 and header
16: Opening and ending tag mismatch: img line 111 and a
17: Opening and ending tag mismatch: a line 110 and span
18: Opening and ending tag mismatch: spa
Execution halted
* 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: 1 ERROR
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/ExpressionAtlas.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ExpressionAtlas
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘ExpressionAtlas’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (ExpressionAtlas)

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(ExpressionAtlas)
Loading required package: Biobase
Loading required package: BiocGenerics

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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


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

The following object is masked from 'package:Biobase':

    rowMedians

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: xml2
> 
> test_check("ExpressionAtlas")
[ FAIL 0 | WARN 2 | SKIP 0 | PASS 3 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 3 ]
> 
> proc.time()
   user  system elapsed 
 12.682   0.557  13.265