Can not use PTXQC due to yml not found

[shuvadeep]

Downloading GitHub repo cbielow/PTXQC@master from URL https://api.github.com/repos/cbielow/PTXQC/zipball/master Installing PTXQC "C:/Users/Vogel_lab/R-3.2.1/bin/x64/R" --no-site-file --no-environ --no-save \ --no-restore --quiet CMD build \ "C:\Users\Vogel_lab\AppData\Local\Temp\Rtmp0ap5qF\devtools2908543220d1\cbielow-PTXQC-7c4baff" \ --no-resave-data --no-manual

• checking for file 'C:\Users\Vogel_lab\AppData\Local\Temp\Rtmp0ap5qF\devtools2908543220d1\cbielow-PTXQC-7c4baff/DESCRIPTION' ... OK
• preparing 'PTXQC':
• checking DESCRIPTION meta-information ... OK
• installing the package to build vignettes
• creating vignettes ...Warning: running command '"C:/Users/VOGEL_~1/R-32~1.1/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1 ERROR Error: processing vignette 'PTXQC-Basic_Guide_for_R_users.Rmd' failed with diagnostics: package 'yaml' not found Execution halted Error: Command failed (1)

[shuvadeep]

Trying to install from from github go the below error " Downloading GitHub repo cbielow/PTXQC@master from URL https://api.github.com/repos/cbielow/PTXQC/zipball/master Installing PTXQC "C:/Users/Vogel_lab/R-3.2.1/bin/x64/R" --no-site-file --no-environ --no-save \ --no-restore --quiet CMD build \ "C:\Users\Vogel_lab\AppData\Local\Temp\Rtmp0ap5qF\devtools2908543220d1\cbielow-PTXQC-7c4baff" \ --no-resave-data --no-manual

• checking for file 'C:\Users\Vogel_lab\AppData\Local\Temp\Rtmp0ap5qF\devtools2908543220d1\cbielow-PTXQC-7c4baff/DESCRIPTION' ... OK
• preparing 'PTXQC':
• checking DESCRIPTION meta-information ... OK
• installing the package to build vignettes
• creating vignettes ...Warning: running command '"C:/Users/VOGEL_~1/R-32~1.1/bin/x64/Rscript" --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)"' had status 1 ERROR Error: processing vignette 'PTXQC-Basic_Guide_for_R_users.Rmd' failed with diagnostics: package 'yaml' not found Execution halted Error: Command failed (1)"

[cbielow]

this is surprising since PTXQC lists YAML as a dependency (https://github.com/cbielow/PTXQC/blob/master/DESCRIPTION#L33).

Can you try to install YAML manually via install.packages("yaml") before installing PTXQC.

I'll grab an R 3.2.1 myself in the next days and try as well, just to confirm.

Thanks for reporting.

[cbielow]

reading the issue again: what command did you use to start the installation?!

[shuvadeep]

Thanks for your answer. I have started installation following this page https://github.com/cbielow/PTXQC/tree/master/inst/dragNdrop https://github.com/cbielow/PTXQC/tree/master/inst/dragNdrop from installation onwards. I have R 3.2.1 so I started with installation pandoc Then PTXQC from github command "## GitHub

if (!require(devtools, quietly = TRUE)) install.packages("devtools") library("devtools") ## this might give a warning like 'WARNING: Rtools is required ...'. Ignore it. install_github("cbielow/PTXQC", build_vignettes = TRUE) ## use build_vignettes = FALSE if you did not install pandoc!

On Mon, Apr 24, 2017 at 3:28 AM, Chris Bielow notifications@github.com wrote:

reading the issue again: what command did you use to start the installation?!

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cbielow/PTXQC/issues/32#issuecomment-296555759, or mute the thread https://github.com/notifications/unsubscribe-auth/AMgQnJc6ADUDkQjziirqqXztknsUBDMaks5rzE8VgaJpZM4NFQXD .

-- shuvadeep Maity

Arise, Awake! And stop not until the goal is reached

[cbielow]

currently, the devtools package seems broken since it cannot build the vignettes properly (at least thats what happens on my machine). If I run install_github("cbielow/PTXQC", build_vignettes = FALSE) all dependent packages seem to get installed. I deleted YAML beforehand and it just re-installs it:

Downloading GitHub repo cbielow/PTXQC@master
from URL https://api.github.com/repos/cbielow/PTXQC/zipball/master
Installing PTXQC
Installing 1 package: yaml
Installing package into ‘C:/Users/bielow/Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/yaml_2.1.14.zip'
Content type 'application/zip' length 179378 bytes (175 KB)
downloaded 175 KB

package ‘yaml’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\bielow\AppData\Local\Temp\RtmpKo2R9r\downloaded_packages
"C:/PROGRA~1/R/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  "C:/Users/bielow/AppData/Local/Temp/RtmpKo2R9r/devtools23b85cc825bb/cbielow-PTXQC-d49f886"  \
  --library="C:/Users/bielow/Documents/R/win-library/3.3" --install-tests 

* installing *source* package 'PTXQC' ...
** R
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PTXQC)

You can also try install_github("cbielow/PTXQC", build_vignettes = FALSE, dependencies = TRUE) to make it explicit.

Let me know if that helps.

[shuvadeep]

Thanks install_github("cbielow/PTXQC", build_vignettes = FALSE, dependencies = TRUE) this works

On Wed, May 3, 2017 at 10:06 AM, Chris Bielow notifications@github.com wrote:

currently, the devtools package seems broken since it cannot build the vignettes properly (at least thats what happens on my machine). If I run install_github("cbielow/PTXQC", build_vignettes = FALSE) all dependent packages seem to get installed. I deleted YAML beforehand and it just re-installs it:

Downloading GitHub repo cbielow/PTXQC@master from URL https://api.github.com/repos/cbielow/PTXQC/zipball/master Installing PTXQC Installing 1 package: yaml Installing package into ‘C:/Users/bielow/Documents/R/win-library/3.3’ (as ‘lib’ is unspecified) trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/yaml_2.1.14.zip' Content type 'application/zip' length 179378 bytes (175 KB) downloaded 175 KB

package ‘yaml’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\bielow\AppData\Local\Temp\RtmpKo2R9r\downloaded_packages "C:/PROGRA~1/R/bin/x64/R" --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ "C:/Users/bielow/AppData/Local/Temp/RtmpKo2R9r/devtools23b85cc825bb/cbielow-PTXQC-d49f886" \ --library="C:/Users/bielow/Documents/R/win-library/3.3" --install-tests

• installing source package 'PTXQC' ... R inst tests preparing package for lazy loading ** help * installing help indices building package indices installing vignettes testing if installed package can be loaded
• DONE (PTXQC)

You can also try install_github("cbielow/PTXQC", build_vignettes = FALSE, dependencies = TRUE) to make it explicit.

Let me know if that helps.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cbielow/PTXQC/issues/32#issuecomment-298921059, or mute the thread https://github.com/notifications/unsubscribe-auth/AMgQnMcwzGlrhNV6tvAJ78Rt1BzkWrGxks5r2InMgaJpZM4NFQXD .

-- shuvadeep Maity

Arise, Awake! And stop not until the goal is reached

[cbielow]

ok. thanks for the feedback. I've changed the installation docs accordingly.