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pkimes / sigclust2

tests for statistical significance of clustering
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Installation issue #7

Closed idc9 closed 5 years ago

idc9 commented 5 years ago

When I install the package using the provided instructions I encounter an error.

> devtools::install_github("pkimes/sigclust2")
Downloading GitHub repo pkimes/sigclust2@master
from URL https://api.github.com/repos/pkimes/sigclust2/zipball/master
Installing sigclust2
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/dplyr_0.7.7.tgz'
Content type 'application/x-gzip' length 5198161 bytes (5.0 MB)
==================================================
downloaded 5.0 MB

Installing dplyr
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/glue_1.3.0.tgz'
Content type 'application/x-gzip' length 93367 bytes (91 KB)
==================================================
downloaded 91 KB

Installing glue
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a6a61d1ea/glue'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

* installing *binary* package ‘glue’ ...
* DONE (glue)
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/pkgconfig_2.0.2.tgz'
Content type 'application/x-gzip' length 15456 bytes (15 KB)
==================================================
downloaded 15 KB

Installing pkgconfig
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a49c2c4c/pkgconfig'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

* installing *binary* package ‘pkgconfig’ ...
* DONE (pkgconfig)
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/R6_2.3.0.tgz'
Content type 'application/x-gzip' length 34492 bytes (33 KB)
==================================================
downloaded 33 KB

Installing R6
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a3f45b26/R6'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

* installing *binary* package ‘R6’ ...
* DONE (R6)
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/Rcpp_0.12.19.tgz'
Content type 'application/x-gzip' length 4429794 bytes (4.2 MB)
==================================================
downloaded 4.2 MB

Installing Rcpp
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a7285bc43/Rcpp'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

* installing *binary* package ‘Rcpp’ ...
* DONE (Rcpp)
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/rlang_0.3.0.1.tgz'
Content type 'application/x-gzip' length 1074663 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

Installing rlang
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a78473bd6/rlang'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

* installing *binary* package ‘rlang’ ...
* DONE (rlang)
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/tidyselect_0.2.5.tgz'
Content type 'application/x-gzip' length 294992 bytes (288 KB)
==================================================
downloaded 288 KB

Installing tidyselect
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a3171858a/tidyselect'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

* installing *binary* package ‘tidyselect’ ...
* DONE (tidyselect)
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a1344b4cb/dplyr'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

* installing *binary* package ‘dplyr’ ...
* DONE (dplyr)
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/ggdendro_0.1-20.tgz'
Content type 'application/x-gzip' length 132139 bytes (129 KB)
==================================================
downloaded 129 KB

Installing ggdendro
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/ggplot2_3.1.0.tgz'
Content type 'application/x-gzip' length 3179264 bytes (3.0 MB)
==================================================
downloaded 3.0 MB

Installing ggplot2
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/digest_0.6.18.tgz'
Content type 'application/x-gzip' length 166752 bytes (162 KB)
==================================================
downloaded 162 KB

Installing digest
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a7ce7e9c/digest'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

* installing *binary* package ‘digest’ ...
* DONE (digest)
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/scales_1.0.0.tgz'
Content type 'application/x-gzip' length 590050 bytes (576 KB)
==================================================
downloaded 576 KB

Installing scales
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a628434f4/scales'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

* installing *binary* package ‘scales’ ...
* DONE (scales)
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a107752db/ggplot2'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

* installing *binary* package ‘ggplot2’ ...
* DONE (ggplot2)
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a9f50133/ggdendro'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

* installing *binary* package ‘ggdendro’ ...
* DONE (ggdendro)
Skipping install of 'ggplot2' from a cran remote, the SHA1 (3.1.0) has not changed since last install.
  Use `force = TRUE` to force installation
trying URL 'https://cran.rstudio.com/bin/macosx/el-capitan/contrib/3.4/ggthemes_4.0.1.tgz'
Content type 'application/x-gzip' length 334081 bytes (326 KB)
==================================================
downloaded 326 KB

Installing ggthemes
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a7a815897/ggthemes'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

* installing *binary* package ‘ggthemes’ ...
* DONE (ggthemes)
Skipping install of 'Rcpp' from a cran remote, the SHA1 (0.12.19) has not changed since last install.
  Use `force = TRUE` to force installation
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ  \
  --no-save --no-restore --quiet CMD INSTALL  \
  '/private/var/folders/tf/8lz5km5n0n509s9y_f1wpj3h0000gn/T/RtmpNU8h6m/devtools1564a4a3a386/pkimes-sigclust2-f5b57f0'  \
  --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library'  \
  --install-tests

ERROR: dependencies ‘Rclusterpp’, ‘WGCNA’ are not available for package ‘sigclust2’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/sigclust2’
Installation failed: Command failed (1)

My R/computer setup is as follows

> R.Version()
$platform
[1] "x86_64-apple-darwin15.6.0"

$arch
[1] "x86_64"

$os
[1] "darwin15.6.0"

$system
[1] "x86_64, darwin15.6.0"

$status
[1] ""

$major
[1] "3"

$minor
[1] "4.3"

$year
[1] "2017"

$month
[1] "11"

$day
[1] "30"

$`svn rev`
[1] "73796"

$language
[1] "R"

$version.string
[1] "R version 3.4.3 (2017-11-30)"

$nickname
[1] "Kite-Eating Tree"
idc9 commented 5 years ago

I updated my R version and get a similar error

> devtools::install_github("pkimes/sigclust2")
Downloading GitHub repo pkimes/sigclust2@master
Skipping 5 packages not available: AnnotationDbi, GO.db, impute, preprocessCore, Rclusterpp
Installing 62 packages: acepack, AnnotationDbi, BH, bindr, bindrcpp, checkmate, colorspace, data.table, DEoptimR, doParallel, dplyr, dynamicTreeCut, evaluate, fansi, fastcluster, fit.models, foreach, Formula, ggdendro, ggplot2, ggthemes, GO.db, gridExtra, gtable, highr, Hmisc, htmlTable, htmltools, htmlwidgets, impute, iterators, knitr, labeling, latticeExtra, lazyeval, markdown, matrixStats, munsell, mvtnorm, pcaPP, pillar, pkgconfig, plogr, plyr, preprocessCore, purrr, Rclusterpp, RColorBrewer, reshape2, robust, robustbase, rrcov, scales, stringi, stringr, tibble, tidyselect, utf8, viridis, viridisLite, WGCNA, yaml
Error: (converted from warning) packages ‘AnnotationDbi’, ‘GO.db’, ‘impute’, ‘preprocessCore’, ‘Rclusterpp’ are not available (for R version 3.5.1)

> R.Version()
$platform
[1] "x86_64-apple-darwin15.6.0"

$arch
[1] "x86_64"

$os
[1] "darwin15.6.0"

$system
[1] "x86_64, darwin15.6.0"

$status
[1] ""

$major
[1] "3"

$minor
[1] "5.1"

$year
[1] "2018"

$month
[1] "07"

$day
[1] "02"

$`svn rev`
[1] "74947"

$language
[1] "R"

$version.string
[1] "R version 3.5.1 (2018-07-02)"

$nickname
[1] "Feather Spray"
pkimes commented 5 years ago

Hi @idc9 - just got a chance to look at this. I think root of your problem is:

  1. Rclusterpp is no longer available on CRAN and needs to be installed from [this GitHub repo].(https://github.com/nolanlab/Rclusterpp)
  2. WGCNA depends on some packages on Bioconductor (‘AnnotationDbi’, ‘GO.db’, ‘impute’, ‘preprocessCore’) and not CRAN.

I'll add a note to the README about Rclusterpp for now, and try to update the package to remove this deprecated dependency when I get a chance.

Thanks for reporting this. Let me know if the above solves your problems!

pkimes commented 5 years ago

I've removed the dependence on Rclusterpp and moved this to "Enhances:" in the DESCRIPTION file in commit 55288e5. The package is no longer required, but if installed, can still be used with sigclust2. The package passed R CMD build/check on machines with and without Rclusterpp installed, so I'm going to close this issue.

Let me know if you still run into issues.

idc9 commented 5 years ago

I'm getting a different error now

> devtools::install_github("pkimes/sigclust2")
Downloading GitHub repo pkimes/sigclust2@master
These packages have more recent versions available.
Which would you like to update?

1:   dplyr (0.7.7 -> 0.7.8) [CRAN]

Enter one or more numbers separated by spaces, or an empty line to cancel
1: 
Installing 26 packages: acepack, checkmate, data.table, DEoptimR, doParallel, dynamicTreeCut, fastcluster, fit.models, foreach, Formula, ggdendro, ggthemes, gridExtra, Hmisc, htmlTable, htmlwidgets, iterators, latticeExtra, matrixStats, mvtnorm, pcaPP, robust, robustbase, rrcov, viridis, WGCNA
Error: (converted from warning) dependencies ‘impute’, ‘preprocessCore’, ‘GO.db’, ‘AnnotationDbi’ are not available
SamGG commented 5 years ago

‘impute’, ‘preprocessCore’, ‘GO.db’, ‘AnnotationDbi’ are Bioconductor packages. I think you should install them first.

pkimes commented 5 years ago

Exactly what @SamGG said. (Thanks @SamGG !)

@idc9, Bioconductor is like CRAN, but contains genomics/bioinformatics packages: http://bioconductor.org/install/

idc9 commented 5 years ago

Ah good point, I should have thought about that. You might add a message to the README e.g.

Some packages need to be installed from Bioconductor

BiocManager::install(c("impute", "preprocessCore", "GO.db", "AnnotationDbi"))
SamGG commented 5 years ago

BTW, one can use BiocManager::install() for Bioconductor's packages but also CRAN's ones and github repos (without devtools). One should try BiocManager::install("pkimes/sigclust2") and maybe everything will be installed smoothly without the need of using different commands depending on the repository.

pkimes commented 5 years ago

Thanks again, @SamGG!

@idc9 - I've updated the README to hopefully make installation easier for users. As pointed out by @SamGG, it looks like installing sigclust2 using a single call to BiocManager::install should handle everything without requiring the user to install the Bioconductor dependencies separately first. (I've verified this on my own machine.) I've changed the recommended installation procedure to reflect this.

SamGG commented 5 years ago

Thanks for your feedback and all your updates.