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RGLab / MAST

Tools and methods for analysis of single cell assay data in R
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install_github fails due to vignette compilation error #34

Closed esimonds closed 10 years ago

esimonds commented 10 years ago

Hi guys, I enjoyed seeing you at CYTO. I tried installing SingleCellAssay using install_github('SingleCellAssay', 'RGLab') on Rstudio 0.97.336 and R version 2.15.3. I got an error relating to the vignette compilation. I installed roxygen2, but that didn't help.

I suspect Sweave's syntax has changed, and your "echo=" arguments are no longer allowed. I was able to resolve the error and install from source through the following steps:

1) Download the .zip 2) Open SingleCellAssay_master/vignettes/SingleCellAssay-intro.Rnw 3) Set all "echo=" to FALSE. This affects lines 66, 142, and 213. 4) Install knitr and plyr packages from CRAN just in case 5) Install SingleCellAssay_master package from source

That may not be the best solution, but hopefully it will point you in the right direction to make installation user-friendly again.

Cheers,

Erin

PS: Console output of the error is below.

> install_github('SingleCellAssay', 'RGLab')
Installing github repo(s) SingleCellAssay/master from RGLab
Installing SingleCellAssay.zip from https://github.com/RGLab/SingleCellAssay/archive/master.zip
Installing SingleCellAssay
Installing dependencies for SingleCellAssay:
data.table
Installing package(s) into ‘/Users/esimonds/Library/R/2.15/library’
(as ‘lib’ is unspecified)

  There is a binary version available (and will be installed) but the source version is later:
           binary source
data.table  1.8.8  1.9.2

trying URL 'http://cran.rstudio.com/bin/macosx/leopard/contrib/2.15/data.table_1.8.8.tgz'
Content type 'application/x-gzip' length 1188814 bytes (1.1 Mb)
opened URL
==================================================
downloaded 1.1 Mb

The downloaded binary packages are in
    /var/folders/cm/8hg79fh52fj5w_h_mmk580tc0000gn/T//Rtmpvm5P3P/downloaded_packages
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD build  \
  '/private/var/folders/cm/8hg79fh52fj5w_h_mmk580tc0000gn/T/Rtmpvm5P3P/SingleCellAssay-master'  \
  --no-manual --no-resave-data 

* checking for file '/private/var/folders/cm/8hg79fh52fj5w_h_mmk580tc0000gn/T/Rtmpvm5P3P/SingleCellAssay-master/DESCRIPTION' ... OK
* preparing 'SingleCellAssay':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Error: processing vignette 'SingleCellAssay-intro.Rnw' failed with diagnostics:
parse error or empty option in
long-example,warning=FALSE, echo=-c(1,2,3)
Execution halted
Error: Command failed (1)
amcdavid commented 10 years ago

Hi Erin , Thanks for checking out the package, and thanks for the bug report . The vignettes only will compile with knitr so i need to modify the package description to enforce that. Can you send me the output of the command sessionInfo() ?

Regards, Andrew On Jun 1, 2014 11:40 AM, "Erin Simonds" notifications@github.com wrote:

Hi guys, I enjoyed seeing you at CYTO. I tried installing SingleCellAssay using install_github('SingleCellAssay', 'RGLab') on Rstudio 0.97.336 and R version 2.15.3. I got an error relating to the vignette compilation. I installed roxygen2, but that didn't help.

I suspect Sweave's syntax has changed, and your "echo=" arguments are no longer allowed. I was able to resolve the error and install from source through the following steps:

1) Download the .zip 2) Open SingleCellAssay_master/vignettes/SingleCellAssay-intro.Rnw 3) Set all "echo=" to FALSE. This affects lines 66, 142, and 213. 4) Install knitr and plyr packages from CRAN just in case 5) Install SingleCellAssay_master package from source

That may not be the best solution, but hopefully it will point you in the right direction to make installation user-friendly again.

Cheers,

Erin

PS: Console output of the error is below.

install_github('SingleCellAssay', 'RGLab')Installing github repo(s) SingleCellAssay/master from RGLabInstalling SingleCellAssay.zip from https://github.com/RGLab/SingleCellAssay/archive/master.zipInstalling SingleCellAssayInstalling dependencies for SingleCellAssay:data.tableInstalling package(s) into ‘/Users/esimonds/Library/R/2.15/library’(as ‘lib’ is unspecified) There is a binary version available (and will be installed) but the source version is later: binary sourcedata.table 1.8.8 1.9.2 trying URL 'http://cran.rstudio.com/bin/macosx/leopard/contrib/2.15/data.table_1.8.8.tgz'Content type 'application/x-gzip' length 1188814 bytes (1.1 Mb)opened URL==================================================downloaded 1.1 Mb

The downloaded binary packages are in /var/folders/cm/8hg79fh52fj5w_h_mmk580tc0000gn/T//Rtmpvm5P3P/downloaded_packages'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD build \ '/private/var/folders/cm/8hg79fh52fj5w_h_mmk580tc0000gn/T/Rtmpvm5P3P/SingleCellAssay-master' \ --no-manual --no-resave-data

  • checking for file '/private/var/folders/cm/8hg79fh52fj5w_h_mmk580tc0000gn/T/Rtmpvm5P3P/SingleCellAssay-master/DESCRIPTION' ... OK* preparing 'SingleCellAssay':* checking DESCRIPTION meta-information ... OK* installing the package to re-build vignettes* creating vignettes ... ERRORError: processing vignette 'SingleCellAssay-intro.Rnw' failed with diagnostics:parse error or empty option inlong-example,warning=FALSE, echo=-c(1,2,3)Execution haltedError: Command failed (1)

— Reply to this email directly or view it on GitHub https://github.com/RGLab/SingleCellAssay/issues/34.

esimonds commented 10 years ago

Sure thing --- this is after an R restart, is that what you meant? I have knitr installed, but I get the same error.

====== console output ======

Restarting R session...

> sessionInfo()

R version 2.15.3 (2013-03-01)
Platform: x86_64-apple-darwin9.8.0/x86_64 (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] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_2.15.3

> install.packages('devtools')
Installing package(s) into ‘/Users/esimonds/Library/R/2.15/library’
(as ‘lib’ is unspecified)
trying URL '
http://cran.rstudio.com/bin/macosx/leopard/contrib/2.15/devtools_1.1.tgz'
Content type 'application/x-gzip' length 228261 bytes (222 Kb)
opened URL
==================================================
downloaded 222 Kb

The downloaded binary packages are in
/var/folders/cm/8hg79fh52fj5w_h_mmk580tc0000gn/T//Rtmp34UaA8/downloaded_packages
> library(devtools)
> install_github('SingleCellAssay', 'RGLab')
Installing github repo(s) SingleCellAssay/master from RGLab
Installing SingleCellAssay.zip from
https://github.com/RGLab/SingleCellAssay/archive/master.zip
Installing SingleCellAssay
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD build  \

'/private/var/folders/cm/8hg79fh52fj5w_h_mmk580tc0000gn/T/Rtmp34UaA8/SingleCellAssay-master'
--no-manual --no-resave-data

* checking for file
'/private/var/folders/cm/8hg79fh52fj5w_h_mmk580tc0000gn/T/Rtmp34UaA8/SingleCellAssay-master/DESCRIPTION'
... OK
* preparing 'SingleCellAssay':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Error: processing vignette 'SingleCellAssay-intro.Rnw' failed with
diagnostics:
parse error or empty option in
long-example,warning=FALSE, echo=-c(1,2,3)
Execution halted
Error: Command failed (1)
> vignette('SingleCellAssay-intro')
Warning message:
vignette ‘SingleCellAssay-intro’ not found

On Sun, Jun 1, 2014 at 5:09 PM, Andrew McDavid notifications@github.com wrote:

Hi Erin , Thanks for checking out the package, and thanks for the bug report . The vignettes only will compile with knitr so i need to modify the package description to enforce that. Can you send me the output of the command sessionInfo() ?

Regards, Andrew On Jun 1, 2014 11:40 AM, "Erin Simonds" notifications@github.com wrote:

Hi guys, I enjoyed seeing you at CYTO. I tried installing SingleCellAssay using install_github('SingleCellAssay', 'RGLab') on Rstudio 0.97.336 and R version 2.15.3. I got an error relating to the vignette compilation. I installed roxygen2, but that didn't help.

I suspect Sweave's syntax has changed, and your "echo=" arguments are no longer allowed. I was able to resolve the error and install from source through the following steps:

1) Download the .zip 2) Open SingleCellAssay_master/vignettes/SingleCellAssay-intro.Rnw 3) Set all "echo=" to FALSE. This affects lines 66, 142, and 213. 4) Install knitr and plyr packages from CRAN just in case 5) Install SingleCellAssay_master package from source

That may not be the best solution, but hopefully it will point you in the right direction to make installation user-friendly again.

Cheers,

Erin

PS: Console output of the error is below.

install_github('SingleCellAssay', 'RGLab')Installing github repo(s) SingleCellAssay/master from RGLabInstalling SingleCellAssay.zip from https://github.com/RGLab/SingleCellAssay/archive/master.zipInstalling SingleCellAssayInstalling dependencies for SingleCellAssay:data.tableInstalling package(s) into ‘/Users/esimonds/Library/R/2.15/library’(as ‘lib’ is unspecified) There is a binary version available (and will be installed) but the source version is later: binary sourcedata.table 1.8.8 1.9.2 trying URL ' http://cran.rstudio.com/bin/macosx/leopard/contrib/2.15/data.table_1.8.8.tgz'Content type 'application/x-gzip' length 1188814 bytes (1.1 Mb)opened URL==================================================downloaded 1.1 Mb

The downloaded binary packages are in /var/folders/cm/8hg79fh52fj5w_h_mmk580tc0000gn/T//Rtmpvm5P3P/downloaded_packages'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD build \ '/private/var/folders/cm/8hg79fh52fj5w_h_mmk580tc0000gn/T/Rtmpvm5P3P/SingleCellAssay-master' \ --no-manual --no-resave-data

  • checking for file '/private/var/folders/cm/8hg79fh52fj5w_h_mmk580tc0000gn/T/Rtmpvm5P3P/SingleCellAssay-master/DESCRIPTION' ... OK* preparing 'SingleCellAssay':* checking DESCRIPTION meta-information ... OK* installing the package to re-build vignettes* creating vignettes ... ERRORError: processing vignette 'SingleCellAssay-intro.Rnw' failed with diagnostics:parse error or empty option inlong-example,warning=FALSE, echo=-c(1,2,3)Execution haltedError: Command failed (1)

— Reply to this email directly or view it on GitHub https://github.com/RGLab/SingleCellAssay/issues/34.

— Reply to this email directly or view it on GitHub https://github.com/RGLab/SingleCellAssay/issues/34#issuecomment-44793591 .

amcdavid commented 10 years ago

Hi Erin,

The option to build vignettes using knitr wasn't added until R3.0. So if you upgrade to 3.0 (or higher, current version is 3.1), the package should build. Or if you are unwilling/unable to upgrade, you might try passing the argument "quick=TRUE" to install_github, but unfortunately I don't have access to a copy of R2.15 to verify if this actually disables vignette construction or not.

I may just need to make R 3.0 a requirement for the package, anyways, since there have been some other strange, under-the-hood changes that have happened that required tweaks to the package that I cannot be certain are backwards-compatible.

Thanks again for the report.

-Andrew