Error Installing

[carmensandoval]

Hi!

I have read your manuscript and am eager to try Embedrr. I am having some trouble installing the package, though, and was wondering if everything looks fine on your end.

I get the following error:

library(devtools)

install_github('davismcc/scater')
Downloading github repo davismcc/scater@master
Error in file(con, "wb") : cannot open the connection
In addition: Warning message:
In file(con, "wb") :
cannot open file '/tmp/RtmpGcdGRV/file16601f73f170.zip': No such file or directory.

install_github('kieranrcampbell/embeddr')
Downloading github repo kieranrcampbell/embeddr@master
Error in file(con, "wb") : cannot open the connection
In addition: Warning message:
In file(con, "wb") :
cannot open file '/tmp/RtmpGcdGRV/file166033aad563.zip': No such file or directory

Thanks!

[kieranrcampbell]

Hi Carmen,

Sounds like you're having trouble connecting to github. Alternatively, you
can git-clone them then install locally, so
$ cd ~/path/you/choose
$ git clone https://github.com/davismcc/scater.git
$ git clone https://github.com/kieranrcampbell/embeddr.git
$ R
$ devtools::install_local("scater")
$ devtools::install_local("embeddr")

Cheers

Kieran

On 23 September 2015 at 01:14, Carmen Sandoval [email protected]
wrote:

Hi!

I have read your manuscript and am eager to try Embedrr. I am having some
trouble installing the package, though, and was wondering if everything
looks fine on your end.

I get the following error:

library(devtools)

install_github('davismcc/scater')
Downloading github repo davismcc/scater@master
Error in file(con, "wb") : cannot open the connection
In addition: Warning message:
In file(con, "wb") :
cannot open file '/tmp/RtmpGcdGRV/file16601f73f170.zip': No such file or
directory.

install_github('kieranrcampbell/embeddr')
Downloading github repo kieranrcampbell/embeddr@master
Error in file(con, "wb") : cannot open the connection
In addition: Warning message:
In file(con, "wb") :
cannot open file '/tmp/RtmpGcdGRV/file166033aad563.zip': No such file or
directory

Thanks!

—
Reply to this email directly or view it on GitHub
#6.

[carmensandoval]

Thanks for your message, Kieran.

I am still having some trouble installing embeddr on my Linux machine. It looks like it has something to do with installing monocle. I've tried installing Monocle separately, but get the same message, after much more verbose.

Any idea what could be going wrong? I am running Fedora 20.

library(devtools)
install_github('davismcc/scater')
Downloading GitHub repo davismcc/scater@master
Installing scater
Installing 2 packages: monocle, viridis
Installing packages into ‘/home/carmensandoval/R/x86_64-redhat-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/monocle_1.0.0.tar.gz'
Content type 'application/x-gzip' length 332309 bytes (324 KB)

downloaded 324 KB

trying URL 'http://cran.rstudio.com/src/contrib/viridis_0.2.5.tar.gz'
Content type 'application/x-gzip' length 133366 bytes (130 KB)

downloaded 130 KB

• installing source package ‘monocle’ ...
  ** R
  ** inst
  ** preparing package for lazy loading
  Error in unloadNamespace(package) :
  namespace ‘plyr’ is imported by ‘reshape2’, ‘ggplot2’, ‘scales’ so cannot be unloaded
  Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
  Package ‘plyr’ version 1.8.1 cannot be unloaded
  ERROR: lazy loading failed for package ‘monocle’
• removing ‘/home/carmensandoval/R/x86_64-redhat-linux-gnu-library/3.2/monocle’
• installing source package ‘viridis’ ...
  ** package ‘viridis’ successfully unpacked and MD5 sums checked
  ** R
  ** data
  *** moving datasets to lazyload DB
  ** inst
  ** preparing package for lazy loading
  ** help
  *** installing help indices
  converting help for package ‘viridis’
  finding HTML links ... done
  scale_viridis html
  Rd warning: /tmp/RtmpfSfZVV/R.INSTALL25ef65e01071/viridis/man/scale_viridis.Rd:24: missing file link ‘scale_fill_gradientn’
  Rd warning: /tmp/RtmpfSfZVV/R.INSTALL25ef65e01071/viridis/man/scale_viridis.Rd:24: missing file link ‘scale_color_gradientn’
  viridis html
  viridis.map html
  viridis_pal html
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded
• DONE (viridis)

The downloaded source packages are in
‘/tmp/RtmpWlInai/downloaded_packages’
'/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore CMD
INSTALL '/tmp/RtmpWlInai/devtools5db3f0b4274/davismcc-scater-e54a75f'
--library='/home/carmensandoval/R/x86_64-redhat-linux-gnu-library/3.2'
--install-tests

ERROR: dependency ‘monocle’ is not available for package ‘scater’

• removing ‘/home/carmensandoval/R/x86_64-redhat-linux-gnu-library/3.2/scater’
  Error: Command failed (1)
  In addition: Warning message:
  In utils::install.packages(pkgs, repos = repos, type = type, ..., :
  installation of package ‘monocle’ had non-zero exit status

[kieranrcampbell]

Hi Carmen,

Thanks for catching this. Monocle is only required for the data to run the
vignette, which I'll remove. In the mean time, you can install monocle and
the companion data package via

source("https://bioconductor.org/biocLite.R")
biocLite("monocle") ; biocLite("HSMMSingleCell")

from within R. Let me know if you have any other problems

Best

Kieran

On 24 September 2015 at 22:31, Carmen Sandoval [email protected]
wrote:

Thanks for your message, Kieran.

I am still having some trouble installing embeddr on my Linux machine. It
looks like it has something to do with installing monocle. I've tried
installing Monocle separately, but get the same message, after much more
verbose.

Any idea what could be going wrong? I am running Fedora 20.

library(devtools)
install_github('davismcc/scater')
Downloading GitHub repo davismcc/scater@master
Installing scater
Installing 2 packages: monocle, viridis
Installing packages into
‘/home/carmensandoval/R/x86_64-redhat-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
trying URL '
http://bioconductor.org/packages/3.0/bioc/src/contrib/monocle_1.0.0.tar.gz
'
Content type 'application/x-gzip' length 332309 bytes (324 KB)

downloaded 324 KB

trying URL 'http://cran.rstudio.com/src/contrib/viridis_0.2.5.tar.gz'
Content type 'application/x-gzip' length 133366 bytes (130 KB)

downloaded 130 KB

• installing source package ‘monocle’ ... ** R ** inst ** preparing
  package for lazy loading Error in unloadNamespace(package) : namespace
  ‘plyr’ is imported by ‘reshape2’, ‘ggplot2’, ‘scales’ so cannot be unloaded
  Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc
  = lib.loc) : Package ‘plyr’ version 1.8.1 cannot be unloaded ERROR: lazy
  loading failed for package ‘monocle’
• removing
  ‘/home/carmensandoval/R/x86_64-redhat-linux-gnu-library/3.2/monocle’
• installing source package ‘viridis’ ... ** package ‘viridis’
  successfully unpacked and MD5 sums checked ** R ** data *** moving datasets
  to lazyload DB ** inst ** preparing package for lazy loading ** help ***
  installing help indices converting help for package ‘viridis’ finding HTML
  links ... done scale_viridis html
  Rd warning:
  /tmp/RtmpfSfZVV/R.INSTALL25ef65e01071/viridis/man/scale_viridis.Rd:24:
  missing file link ‘scale_fill_gradientn’ Rd warning:
  /tmp/RtmpfSfZVV/R.INSTALL25ef65e01071/viridis/man/scale_viridis.Rd:24:
  missing file link ‘scale_color_gradientn’ viridis html
  viridis.map html
  viridis_pal html
  ** building package indices ** installing vignettes ** testing if
  installed package can be loaded
• DONE (viridis)

The downloaded source packages are in
‘/tmp/RtmpWlInai/downloaded_packages’
'/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore
CMD
INSTALL '/tmp/RtmpWlInai/devtools5db3f0b4274/davismcc-scater-e54a75f'
--library='/home/carmensandoval/R/x86_64-redhat-linux-gnu-library/3.2'
--install-tests

ERROR: dependency ‘monocle’ is not available for package ‘scater’

• removing
  ‘/home/carmensandoval/R/x86_64-redhat-linux-gnu-library/3.2/scater’ Error:
  Command failed (1) In addition: Warning message: In
  utils::install.packages(pkgs, repos = repos, type = type, ..., :
  installation of package ‘monocle’ had non-zero exit status

—
Reply to this email directly or view it on GitHub
#6 (comment)
.

[carmensandoval]

Thanks, Kieran.

Unfortunately, when I try to install monocle independently, I still get the same error.

biocLite("monocle")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.0.
Installing package(s) 'monocle'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/monocle_1.0.0.tar.gz'
Content type 'application/x-gzip' length 332309 bytes (324 KB)
downloaded 324 KB

installing source package ‘monocle’ ...

R
inst
preparing package for lazy loading

Error in unloadNamespace(package) :

namespace ‘plyr’ is imported by ‘reshape2’, ‘ggplot2’, ‘scales’ so cannot be unloaded

Error in library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) :
Package ‘plyr’ version 1.8.1 cannot be unloaded
ERROR: lazy loading failed for package ‘monocle’
removing ‘/home/carmensandoval/R/x86_64-redhat-linux-gnu-library/3.2/monocle’

[kieranrcampbell]

Can you restart R and try again? And if it fails post the results of sessionInfo()

Cheers

Kieran

[carmensandoval]

Hi,

I restarted everything and still get the same error... not sure what it means. Here are the results of sessionInfo():

sessionInfo()

R version 3.2.0 (2015-04-16)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Fedora 20 (Heisenbug)

locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

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

other attached packages:
[1] devtools_1.9.1

loaded via a namespace (and not attached):
[1] httr_1.0.0 R6_2.1.1 magrittr_1.5
[4] BiocInstaller_1.16.5 tools_3.2.0 curl_0.9.3
[7] memoise_0.2.1 stringi_0.5-5 knitr_1.11
[10] stringr_1.0.0 digest_0.6.8

Thanks again,

Carmen