Installation issue

Question

Installation issue

Closed this issue 4 years ago · 18 comments

When installing, I have following errors and failed.

Downloading GitHub repo aertslab/SCopeLoomR@master
from URL https://api.github.com/repos/aertslab/SCopeLoomR/zipball/master
Installing SCopeLoomR
Installing 1 package: rjson
Warning message:
"unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.5:
cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.5/PACKAGES'"

Answer 1 · 2018-12-02T03:41:19.000Z

Also
I failed to install HDF5 with following errors
Error in parse(text = x, srcfile = src): :1:6: unexpected symbol
1: wget https
^
Traceback:

Answer 2 · 2018-12-02T11:51:52.000Z

Installing HDF5 the way it's described in the README.md is not going to work for Windows.
Try to install HDF5 using prebuilt libraries available at https://www.hdfgroup.org/downloads/hdf5/.

Answer 3 · 2018-12-03T01:13:02.000Z

Thanks.
Also, doMC cannot be installed may be also because I am using Windows.

Does subsequent analysis depend on doMC or if there are any substitution?

Answer 4 · 2018-12-03T01:27:21.000Z

I tried Mac computer, but saw an error.
Error in parse(text = x, srcfile = src): :1:6: unexpected symbol
1: wget https
^
Traceback:

Answer 5 · 2018-12-03T08:47:36.000Z

wget is not going to work neither on Mac OS except if you have installed it (see https://www.mkyong.com/mac/wget-on-mac-os-x/).

I have updated the README.md to use curl which should be compatible by default on Linux and MacOS machines.

Indeed doMC does not work for Windows and it is not required by SCopeLoomR so you can omit its installation.

Answer 6 · 2018-12-03T21:29:25.000Z

About hdf5, is hdf5r sufficient?
Installation error for aertslab/SCopeLoomR partially come from the lastest version of R.
After reinstall older version (R3.4.3), the install_github("aertslab/SCopeLoomR") started to run, but caused error because of existing Rcpp package.
In addition, for some reason, install_github("aertslab/SCopeLoomR") crashed R and I reinstalled, R and anaconda again.
It might help if I can install SCopeLoomR without installing Rcpp.
Do you have advice?

Answer 7 · 2018-12-03T23:04:11.000Z

The R package hdf5r requires HDF5 library to be installed. So if you can install the R package correctly, then it should be fine.
I don't follow you. Could you post the steps and the stack trace showing clearly the error you get?

Answer 8 · 2018-12-03T23:56:38.000Z

The problem seems that installation causes corruption in some packages that I already installed via installation of Seurat.

Before installation of SCopeLoomR and SCENIC
packageVersion("Rtsne")
packageVersion("mixtools")
packageVersion("Rcpp")
gives
[1] '0.15'

[1] '1.1.0'

[1] '0.12.18'

biocLite(c("GENIE3", "RcisTarget", "AUCell")) caused no issue
biocLite(c("mixtools")). caused issue on mixtools
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02).
Installing package(s) 'mixtools'

package 'mixtools' successfully unpacked and MD5 sums checked

Warning message:
"cannot remove prior installation of package 'mixtools'"

and
packageVersion("mixtools")
gives
Error in packageVersion("mixtools"): package 'mixtools' not found

biocLite(c("NMF", "Rtsne", "R2HTML")) caused issue on Rtsne

BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.1 (2018-07-02).
Installing package(s) 'NMF', 'Rtsne', 'R2HTML'

package 'NMF' successfully unpacked and MD5 sums checked
package 'Rtsne' successfully unpacked and MD5 sums checked

Warning message:
"cannot remove prior installation of package 'Rtsne'"

package 'R2HTML' successfully unpacked and MD5 sums checked

and
packageVersion( "Rtsne")
gives
Error in packageVersion("Rtsne"): package 'Rtsne' not found

install_github("aertslab/SCopeLoomR",repos=c(CRAN="https://cran.cnr.berkeley.edu/")) caused issue on Rcpp

Downloading GitHub repo aertslab/SCopeLoomR@master

Rcpp (NA -> 1.0.0 ) [CRAN]
rjson (NA -> 0.2.20 ) [CRAN]
rlist (NA -> 0.4.6.1) [CRAN]

Installing 3 packages: Rcpp, rjson, rlist

package 'Rcpp' successfully unpacked and MD5 sums checked

Error: (converted from warning) cannot remove prior installation of package 'Rcpp'
Traceback:

install_github("aertslab/SCopeLoomR", repos = c(CRAN = "https://cran.cnr.berkeley.edu/"))
install_remotes(remotes, auth_token = auth_token, host = host,
. dependencies = dependencies, upgrade = upgrade, force = force,
. quiet = quiet, build = build, build_opts = build_opts, repos = repos,
. type = type, ...)
vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
FUN(X[[i]], ...)
install(source, dependencies = dependencies, upgrade = upgrade,
. force = force, quiet = quiet, build = build, build_opts = build_opts,
. repos = repos, type = type, ...)
install_deps(pkgdir, dependencies = dependencies, quiet = quiet,
. build = build, build_opts = build_opts, upgrade = upgrade,
. repos = repos, type = type, ...)
update(packages, dependencies = dep_deps, quiet = quiet, upgrade = upgrade,
. build = build, build_opts = build_opts, ...)
update.package_deps(packages, dependencies = dep_deps, quiet = quiet,
. upgrade = upgrade, build = build, build_opts = build_opts,
. ...)
install_packages(object$package[object$is_cran & behind], repos = attr(object,
. "repos"), type = attr(object, "type"), dependencies = dependencies,
. quiet = quiet, ...)
do.call(safe_install_packages, c(list(packages, repos = repos,
. type = type, dependencies = dependencies, quiet = quiet),
. args))
(function (...)
. {
. lib <- paste(.libPaths(), collapse = ":")
. if (has_package("crancache") && has_package("callr")) {
. i.p <- "crancache" %::% "install_packages"
. }
. else {
. i.p <- utils::install.packages
. }
. with_envvar(c(R_LIBS = lib, R_LIBS_USER = lib, R_LIBS_SITE = lib),
. if (should_error_for_warnings()) {
. with_options(list(warn = 2), with_rprofile_user("options(warn = 2)",
. i.p(...)))
. }
. else {
. i.p(...)
. })
. })(c("Rcpp", "rjson", "rlist"), repos = c(CRAN = "https://cran.cnr.berkeley.edu/"),
. type = "both", dependencies = NA, quiet = FALSE)
with_envvar(c(R_LIBS = lib, R_LIBS_USER = lib, R_LIBS_SITE = lib),
. if (should_error_for_warnings()) {
. with_options(list(warn = 2), with_rprofile_user("options(warn = 2)",
. i.p(...)))
. } else {
. i.p(...)
. })
force(code)
with_options(list(warn = 2), with_rprofile_user("options(warn = 2)",
. i.p(...)))
force(code)
with_rprofile_user("options(warn = 2)", i.p(...))
with_envvar(c(R_PROFILE_USER = temp_rprofile), {
. force(code)
. })
force(code)
force(code)
i.p(...)
.install.winbinary(pkgs = bins, lib = lib, contriburl = contrib.url(repos,
. type2), method = method, available = av2, destdir = destdir,
. dependencies = NULL, libs_only = libs_only, quiet = quiet,
. ...)
unpackPkgZip(foundpkgs[okp, 2L], foundpkgs[okp, 1L], lib, libs_only,
. lock)
warning(gettextf("cannot remove prior installation of package %s",
. sQuote(pkgname)), domain = NA, call. = FALSE, immediate. = TRUE)
.signalSimpleWarning("cannot remove prior installation of package 'Rcpp'",
. quote(NULL))
withRestarts({
. .Internal(.signalCondition(simpleWarning(msg, call), msg,
. call))
. .Internal(.dfltWarn(msg, call))
. }, muffleWarning = function() NULL)
withOneRestart(expr, restarts[[1L]])
doWithOneRestart(return(expr), restart)

and now
packageVersion("Rcpp")
gives
Error in packageVersion("Rcpp"): package 'Rcpp' not found
Traceback:
6. corruption of Rcpp caused malfunction of R in jupyternotebook
I need to reinstall everything to fix this.

Can you really successfully install SCopeLoomR and SCENIC on PC of windows 10?

thanks for reading this long comment!

Answer 9 · 2018-12-04T00:15:04.000Z

I will have to test this on a Windows machine to try to reproduce your error. Meanwhile, I would consider to check this post https://stackoverflow.com/questions/26570912/error-in-installation-a-r-package. This could potentially solve the multiple "cannot remove prior installation of package 'X'" issues you encounter.

Answer 10 · 2018-12-04T02:10:00.000Z

Thanks for the advice.
In addition, I used my Mac computer to install ScopeLoomR, but got the following error.

Downloading GitHub repo aertslab/SCopeLoomR@master
from URL https://api.github.com/repos/aertslab/SCopeLoomR/zipball/master
Installing SCopeLoomR
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/hd/jfvg2qw96kn9xd2bqqjjshhm0000gn/T/RtmpqdHEzT/devtools10f0b225a9501/aertslab-SCopeLoomR-b999d1e'
--library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library'
--install-tests

Answer 11 · 2018-12-05T14:56:22.000Z

Downloading GitHub repo aertslab/SCopeLoomR@master
from URL https://api.github.com/repos/aertslab/SCopeLoomR/zipball/master
Installing SCopeLoomR
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ
--no-save --no-restore --quiet CMD INSTALL
'/private/var/folders/hd/jfvg2qw96kn9xd2bqqjjshhm0000gn/T/RtmpqdHEzT/devtools10f0b225a9501/aertslab-SCopeLoomR-b999d1e'
--library='/Library/Frameworks/R.framework/Versions/3.5/Resources/library'
--install-tests

This doesn't seem to be an error...

Answer 12 · 2018-12-05T17:02:57.000Z

packageVersion("aertslab/SCopeLoomR")
gives
Error in packageVersion("aertslab/SCopeLoomR"): package ‘aertslab/SCopeLoomR’ not found

Seems to be common errors such as in catavallejos/BASiCS#9

My colleague also failed to install SCopeLoomR and SCENIC.

Answer 13 · 2018-12-05T17:12:15.000Z

packageVersion("aertslab/SCopeLoomR") is not going to work. You should do packageVersion("SCopeLoomR")

Answer 14 · 2018-12-05T17:21:29.000Z

There's been an issue regarding installation of SCopeLoomR in a recent post. Maybe try this to install SCopeLoomR like this:

install_github("aertslab/SCopeLoomR", repos = c(CRAN = "https://cran.cnr.berkeley.edu/"))

Regarding SCENIC, It seems that recent versions of feather is causing some problems on Windows.
Try to install first feather (version 0.3.1) using this snippet before installing SCENIC:

install.packages("https://cran.r-project.org/bin/windows/contrib/3.4/feather_0.3.1.zip", repos=NULL)

Answer 15 · 2018-12-06T01:53:37.000Z

Thanks for the advice.
I now successfully installed ScopeLoomR and SCENIC in the my Mac computer.

But I still had trouble with installing ScopeLoomR (error is "Error: (converted from warning) cannot remove prior installation of package 'Rcpp").
It tries to install Rcpp package that causes crashing my R. If there is a way to install ScopeLoomR without installing Rcpp, it might help.

Answer 16 · 2018-12-06T08:54:47.000Z

SCopeLoomR is not dependent on Rcpp. I think the problem arise from devtools which requires Rcpp. Maybe devtools wasn't not correctly installed.. Maybe try to remove Rcpp package and devtools and reinstall devtools:

remove.packages("devtools)
install.packages("devtools")
devtools::install_github("aertslab/SCopeLoomR")

Another way to install SCopeLoomR is by downloading the binary: https://github.com/aertslab/SCopeLoomR/releases/download/v0.3.1/SCopeLoomR_0.3.1.tar.gz.
Then in RStudio, you could install it by running:

install.packages("SCopeLoomR_0.3.1.tar.gz", repos = NULL, type="source")

Answer 17 · 2018-12-06T21:54:08.000Z

Thanks for the advice!

As you pointed out, it seems that install_github crashes R in my case. (I did not notice this as I used install.packages for most of packages).
Some people also had similar issues r-lib/devtools#524
I tried some of the procedures posted there, but so far I did not have any lucks.

I also tried install.packages("path to the file/SCopeLoomR_0.3.1.tar.gz", repos = NULL, type="source") , but I got
Warning message in install.packages("F:/UNC/Dropseq/software/test/SCopeLoomR_0.3.1.tar.gz", :
"installation of package 'F:/UNC/Dropseq/software/test/SCopeLoomR_0.3.1.tar.gz' had non-zero exit status"
I looked into this issues, but have not had any luck.

I will use my Mac computer for SCENIC in the mean time to solve this issue.

Answer 18 · 2018-12-06T23:17:31.000Z

I finally installed ScopeLoomR through
Rcmd INSTALL Desktop/SCopeLoomR_0.3.1.tar.gz
at localhost command window

Do you also have the binary download link for SCENIC? It seems that I do not have luck for SCENIC too from github.
thanks.