Can't run unit tests: "Error in library(testthat) : there is no package called ‘testthat’"

[jrvalcourt]

Hi,

I'm trying to install subSeq using R 3.1.1 on OS X Yosemite. I get a few warnings during installation, and then I can't run the unit tests. They fail with the following error: "Error in library(testthat) : there is no package called ‘testthat’"

Here's my full session:

R version 3.1.1 (2014-07-10) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.1.0 (64-bit)

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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.

[R.app GUI 1.65 (6784) x86_64-apple-darwin13.1.0]

[Workspace restored from /Users/jrvalcourt/.RData]
[History restored from /Users/jrvalcourt/.Rapp.history]

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help
> biocLite(c("limma", "edgeR", "DESeq2", "DEXSeq", "pasilla"))
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.1.
Installing package(s) 'limma' 'edgeR' 'DESeq2' 'DEXSeq' 'pasilla'
trying URL 'http://bioconductor.org/packages/2.14/bioc/bin/macosx/mavericks/contrib/3.1/limma_3.20.9.tgz'
Content type 'application/x-gzip' length 1770784 bytes (1.7 Mb)
opened URL
==================================================
downloaded 1.7 Mb

trying URL 'http://bioconductor.org/packages/2.14/bioc/bin/macosx/mavericks/contrib/3.1/edgeR_3.6.8.tgz'
Content type 'application/x-gzip' length 1170654 bytes (1.1 Mb)
opened URL
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downloaded 1.1 Mb

trying URL 'http://bioconductor.org/packages/2.14/bioc/bin/macosx/mavericks/contrib/3.1/DESeq2_1.4.5.tgz'
Content type 'application/x-gzip' length 1261239 bytes (1.2 Mb)
opened URL
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downloaded 1.2 Mb

trying URL 'http://bioconductor.org/packages/2.14/bioc/bin/macosx/mavericks/contrib/3.1/DEXSeq_1.10.8.tgz'
Content type 'application/x-gzip' length 525971 bytes (513 Kb)
opened URL
==================================================
downloaded 513 Kb

trying URL 'http://bioconductor.org/packages/2.14/data/experiment/bin/macosx/mavericks/contrib/3.1/pasilla_0.4.0.tgz'
Content type 'application/x-gzip' length 4015543 bytes (3.8 Mb)
opened URL
==================================================
downloaded 3.8 Mb


The downloaded binary packages are in
    /var/folders/37/7yxlz2lx3jqbrvf_z5cf4v080000gn/T//RtmpKOSHKJ/downloaded_packages
> install.packages("devtools")
--- Please select a CRAN mirror for use in this session ---
trying URL 'http://cran.mirrors.hoobly.com/bin/macosx/mavericks/contrib/3.1/devtools_1.6.tgz'
Content type 'application/x-gzip' length 271197 bytes (264 Kb)
opened URL
==================================================
downloaded 264 Kb


The downloaded binary packages are in
    /var/folders/37/7yxlz2lx3jqbrvf_z5cf4v080000gn/T//RtmpKOSHKJ/downloaded_packages
> library(devtools)
> install_github("qvalue", "jdstorey")
Downloading github repo jdstorey/qvalue@master
Installing qvalue
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL '/private/var/folders/37/7yxlz2lx3jqbrvf_z5cf4v080000gn/T/RtmpKOSHKJ/devtools10ee6f92257/jdstorey-qvalue-7608f5e'  \
  --library='/Library/Frameworks/R.framework/Versions/3.1/Resources/library' --install-tests 

* installing *source* package ‘qvalue’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qvalue)
Warning message:
Username parameter is deprecated. Please use jdstorey/qvalue 
> install_github("subSeq", "StoreyLab")
Downloading github repo StoreyLab/subSeq@master
Installing subSeq
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL '/private/var/folders/37/7yxlz2lx3jqbrvf_z5cf4v080000gn/T/RtmpKOSHKJ/devtools10ee27f5d9ed/StoreyLab-subSeq-0fadc9e'  \
  --library='/Library/Frameworks/R.framework/Versions/3.1/Resources/library' --install-tests 

* installing *source* package ‘subSeq’ ...
** R
** data
** inst
** tests
** preparing package for lazy loading
Warning: replacing previous import by ‘dplyr::last’ when loading ‘subSeq’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘dplyr::last’ when loading ‘subSeq’
* DONE (subSeq)
Warning message:
Username parameter is deprecated. Please use StoreyLab/subSeq 
> library(testthat)
Error in library(testthat) : there is no package called ‘testthat’
> test_package("subSeq")
Error: could not find function "test_package"

Any idea where I'm going wrong? Thanks for your help!

[dgrtwo]

Install the testthat package first, with:

install.packages("testthat")

[jrvalcourt]

Ah, that should have been obvious, thanks. Then I immediately hit this issue:
> library(testthat)
> test_package("subSeq")
Error in eval(expr, envir, enclos) : object 'hammer' not found
In addition: Warning messages:
1: replacing previous import by ‘dplyr::last’ when loading ‘subSeq’
2: In data(hammer) : data set ‘hammer’ not found

And the vignette doesn't seem to work either:
> library(subSeq)
> vignette("subSeq")
Warning message:
vignette ‘subSeq’ not found

[dgrtwo]

The first is simply because you didn't run library(subSeq) before test_package("subSeq").

The latter is more surprising to me. Could you please run the line find.package("subSeq"), which will give you a directory, then look inside that directory in the doc folder, and see if a file subSeq.pdf is present?

[jrvalcourt]

Thanks for bearing with me. I ran the test, but it hit an error. Is it something I should worry about?

......
Subsampling : ....................................
Custom Handlers : .......1...................................
Reproducibility from seeds : .................
Plotting : .
Error handling : .........


1. Error: Can provide custom error handlers -------------------------------------------------------------------------------------------------------------------------------------------------------------------------
object 'depth' not found
1: withCallingHandlers(eval(code, new_test_environment), error = capture_calls)
2: eval(code, new_test_environment)
3: eval(expr, envir, enclos)
4: expect_equal(fake.pvalues, ss.custom[depth == min(depth)]$pvalue) at test-subSeq.R:212
5: expect_that(object, equals(expected, label = expected.label, ...), info = info, label = label)
6: condition(object)
7: compare(expected, actual, ...)
8: ss.custom[depth == min(depth)]
9: `[.data.table`(ss.custom, depth == min(depth))
10: eval(isub[[3L]], parent.frame())
11: eval(expr, envir, enclos)
12: .handleSimpleError(function (e) 
   {
   e$calls <- head(sys.calls()[-seq_len(frame + 7)], -2)
   signalCondition(e)
   }, "object 'depth' not found", quote(eval(expr, envir, enclos)))

Error: Test failures
In addition: Warning messages:
1: In log(ifelse(y == 0, 1, y/mu)) : NaNs produced
2: step size truncated due to divergence 

As for the vignette issue, it appears that the PDF is in the right place:

> find.package("subSeq")
[1] "/Library/Frameworks/R.framework/Versions/3.1/Resources/library/subSeq"

And the documentation is in

/Library/Frameworks/R.framework/Versions/3.1/Resources/library/subSeq/doc/subSeq.pdf

as it should be.

[dgrtwo]

I believe the test failure is a bug introduced by a data.table version, and I think I fixed it with this commit (thanks for finding it!!)

I am puzzled by the vignette issue. Could you try two things. First:

browseVignettes("subSeq")

See if that shows it as available. Second, please try (re)installing with

devtools::install_github("subSeq", build_vignettes = TRUE)

[jrvalcourt]

This doesn't show any vignettes:

> browseVignettes("subSeq")
No vignettes found by browseVignettes("subSeq")

But that's not surprising once you see what happens during the rebuild:

> devtools::install_github("subSeq", "StoreyLab", build_vignettes = TRUE)
Downloading github repo StoreyLab/subSeq@master
Installing subSeq
Installing dependencies for subSeq:
knitr, knitr
also installing the dependencies ‘mime’, ‘formatR’, ‘highr’, ‘markdown’

trying URL 'http://cran.mirrors.hoobly.com/bin/macosx/mavericks/contrib/3.1/mime_0.2.tgz'
Content type 'application/x-gzip' length 22743 bytes (22 Kb)
opened URL
==================================================
downloaded 22 Kb

trying URL 'http://cran.mirrors.hoobly.com/bin/macosx/mavericks/contrib/3.1/formatR_1.0.tgz'
Content type 'application/x-gzip' length 43458 bytes (42 Kb)
opened URL
==================================================
downloaded 42 Kb

trying URL 'http://cran.mirrors.hoobly.com/bin/macosx/mavericks/contrib/3.1/highr_0.3.tgz'
Content type 'application/x-gzip' length 26097 bytes (25 Kb)
opened URL
==================================================
downloaded 25 Kb

trying URL 'http://cran.mirrors.hoobly.com/bin/macosx/mavericks/contrib/3.1/markdown_0.7.4.tgz'
Content type 'application/x-gzip' length 166004 bytes (162 Kb)
opened URL
==================================================
downloaded 162 Kb

trying URL 'http://cran.mirrors.hoobly.com/bin/macosx/mavericks/contrib/3.1/knitr_1.6.tgz'
Content type 'application/x-gzip' length 899423 bytes (878 Kb)
opened URL
==================================================
downloaded 878 Kb


The downloaded binary packages are in
    /var/folders/37/7yxlz2lx3jqbrvf_z5cf4v080000gn/T//RtmpaDgozA/downloaded_packages
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD build '/private/var/folders/37/7yxlz2lx3jqbrvf_z5cf4v080000gn/T/RtmpaDgozA/devtoolsbad424bf2cf/StoreyLab-subSeq-cf4a969' --no-manual  \
  --no-resave-data 

* checking for file ‘/private/var/folders/37/7yxlz2lx3jqbrvf_z5cf4v080000gn/T/RtmpaDgozA/devtoolsbad424bf2cf/StoreyLab-subSeq-cf4a969/DESCRIPTION’ ... OK
* preparing ‘subSeq’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Warning: 'function (...) 
{
    .Deprecated("tidy_source", package = "formatR")
    tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help("Deprecated") and help("formatR-deprecated").
Warning: replacing previous import by 'dplyr::last' when loading 'subSeq'
Warning: 'function (...) 
{
    .Deprecated("tidy_source", package = "formatR")
    tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help("Deprecated") and help("formatR-deprecated").
Warning: 'function (...) 
{
    .Deprecated("tidy_source", package = "formatR")
    tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help("Deprecated") and help("formatR-deprecated").
Warning: 'function (...) 
{
    .Deprecated("tidy_source", package = "formatR")
    tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help("Deprecated") and help("formatR-deprecated").
Warning: 'function (...) 
{
    .Deprecated("tidy_source", package = "formatR")
    tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help("Deprecated") and help("formatR-deprecated").
Loading required package: edgeR
Loading required package: limma
Warning: 'function (...) 
{
    .Deprecated("tidy_source", package = "formatR")
    tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help("Deprecated") and help("formatR-deprecated").
Warning: 'function (...) 
{
    .Deprecated("tidy_source", package = "formatR")
    tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help("Deprecated") and help("formatR-deprecated").
Warning: 'function (...) 
{
    .Deprecated("tidy_source", package = "formatR")
    tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help("Deprecated") and help("formatR-deprecated").
Warning: 'function (...) 
{
    .Deprecated("tidy_source", package = "formatR")
    tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help("Deprecated") and help("formatR-deprecated").
Warning: 'function (...) 
{
    .Deprecated("tidy_source", package = "formatR")
    tidy_source(...)
Error: Command failed (1)
In addition: Warning message:
Username parameter is deprecated. Please use StoreyLab/subSeq 
}' is deprecated.
Use 'tidy_source' instead.
See help("Deprecated") and help("formatR-deprecated").
Warning: 'function (...) 
{
    .Deprecated("tidy_source", package = "formatR")
    tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help("Deprecated") and help("formatR-deprecated").
Loading required package: splines
Warning: 'function (...) 
{
    .Deprecated("tidy_source", package = "formatR")
    tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help("Deprecated") and help("formatR-deprecated").
Warning: 'function (...) 
{
    .Deprecated("tidy_source", package = "formatR")
    tidy_source(...)
}' is deprecated.
Use 'tidy_source' instead.
See help("Deprecated") and help("formatR-deprecated").
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'subSeq.tex' failed.
Calls: <Anonymous> -> texi2pdf -> texi2dvi
Execution halted

And you're right, your most recent commit fixed the test cases for me, thanks!

[dgrtwo]

Interesting; I can't reproduce this error but this appears to be related. Could you

a) Try reinstalling knitr and rmarkdown (using install.packages) before installing it again
b) Sharing the output of sessionInfo() from your R, so I can see what version of packages you have?

[jrvalcourt]

No such luck; doing

install.packages("rmarkdown")

and

install.packages("knitr")    

before rebuilding doesn't help. Here's my sessionInfo() output:

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  splines   stats     graphics  grDevices utils     datasets  methods   base 

other attached packages:
 [1] subSeq_0.99.0             devtools_1.6.1            DEXSeq_1.10.8             BiocParallel_0.6.1        Biobase_2.24.0            DESeq2_1.4.5              RcppArmadillo_0.4.450.1.0 Rcpp_0.11.3          
 [9] GenomicRanges_1.16.4      GenomeInfoDb_1.0.2        IRanges_1.22.10           BiocGenerics_0.10.0       edgeR_3.6.8               limma_3.20.9              testthat_0.9.1       

loaded via a namespace (and not attached):
 [1] annotate_1.42.1      AnnotationDbi_1.26.1 assertthat_0.1       base64enc_0.1-2      BatchJobs_1.4        BBmisc_1.7           biomaRt_2.20.0       Biostrings_2.32.1    bitops_1.0-6    
[10] brew_1.0-6           checkmate_1.4        chron_2.3-45         codetools_0.2-9      colorspace_1.2-4     data.table_1.9.4     DBI_0.3.1            digest_0.6.4         dplyr_0.2       
[19] evaluate_0.5.5       fail_1.2             foreach_1.4.2        formatR_1.0          genefilter_1.46.1    geneplotter_1.42.0   ggplot2_1.0.0        grid_3.1.1           gtable_0.1.2    
[28] httr_0.5             hwriter_1.3.2        iterators_1.0.7      knitr_1.6            lattice_0.20-29      locfit_1.5-9.1       magrittr_1.0.1       MASS_7.3-35          munsell_0.4.2   
[37] plyr_1.8.1           proto_0.3-10         qvalue_1.99.0        RColorBrewer_1.0-5   RCurl_1.95-4.3       reshape2_1.4         Rsamtools_1.16.1     RSQLite_0.11.4       scales_0.2.4    
[46] sendmailR_1.2-1      statmod_1.4.20       stats4_3.1.1         stringr_0.6.2        survival_2.37-7      tidyr_0.1            tools_3.1.1          XML_3.98-1.1         xtable_1.7-4    
[55] XVector_0.4.0        zlibbioc_1.10.0

But I think at this point I can go ahead and start using subSeq, since it's just having trouble building the docs, right?

[dgrtwo]

That's right (and since you can find the vignette in the package itself). I'm sorry we couldn't fix it, though! I'll wait and see if it appears again...

[jrvalcourt]

No worries. Thanks a bunch for your help!