[SOLVED] problems with jmvtools::install() and jmvtools::cre

Everything related to the development of modules in jamovi
User avatar
jonathon
Posts: 2613
Joined: Fri Jan 27, 2017 10:04 am

Re: problems with jmvtools::install() and jmvtools::create()

Post by jonathon »

i have to admit, i'm finding this bug pretty bewildering.

i've just pushed out a new jmvtools, could you try this one too?

with thanks
pedrak
Posts: 16
Joined: Tue Apr 11, 2017 7:54 am

Re: problems with jmvtools::install() and jmvtools::create()

Post by pedrak »

Hi Jonathon,
I am really sorry to create you all these troubles. I am using two different computers, one with windows 7 and the other with windows 10. The errors are the same on both, so I guess they do not depend on the particular OS.
Even after the last jmvtools version the output is the same

> jmvtools::install()

jamovi compiler

jamovi found at C:\Program Files\jamovi 0.7.3.0 Beta 3\bin\jamovi.exe
wrote: anova.h.R
wrote: anova.src.js
wrote: anova.js
wrote: ttestis.h.R
wrote: ttestis.src.js
wrote: ttestis.js
wrote: ttestones.h.R
wrote: ttestones.src.js
wrote: ttestones.js
wrote: ttestps.h.R
wrote: ttestps.src.js
wrote: ttestps.js
writing module meta
wrote: 0000.yaml
wrote: jamovi.yaml

Error: EBUSY: resource busy or locked, read

Warning message:
running command '"C:/Users/GPedra/Documents/R/win-library/3.3/node/node.exe" "C:/Users/GPedra/Documents/R/win-library/3.3/jmvtools/node_modules/jamovi-compiler/index.js" --install "." --home "C:\Program Files\jamovi 0.7.3.0 Beta 3\bin"' had status 1


-------------

In case might be helpful, these are the output from the 'build' subpanel in Rstudio


==> devtools::test()

Error: No testthat directories found in C:\Users\GPedra\Desktop\jmvbaseR-master
Execution halted

Exited with status 1.




==> devtools::check(document = FALSE)

Setting env vars ---------------------------------------------------------------
CFLAGS : -Wall -pedantic
CXXFLAGS: -Wall -pedantic
Building jmvbaseR --------------------------------------------------------------
"C:/PROGRA~1/R/R-33~1.3/bin/x64/R" --no-site-file --no-environ --no-save \
--no-restore --quiet CMD build "C:\Users\GPedra\Desktop\jmvbaseR-master" \
--no-resave-data --no-manual

* checking for file 'C:\Users\GPedra\Desktop\jmvbaseR-master/DESCRIPTION' ... OK
* preparing 'jmvbaseR':
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
Removed empty directory 'jmvbaseR/build/R'
* building 'jmvbaseR_0.2.0.tar.gz'

Setting env vars ---------------------------------------------------------------
_R_CHECK_CRAN_INCOMING_ : FALSE
_R_CHECK_FORCE_SUGGESTS_: FALSE
Checking jmvbaseR --------------------------------------------------------------
"C:/PROGRA~1/R/R-33~1.3/bin/x64/R" --no-site-file --no-environ --no-save \
--no-restore --quiet CMD check \
"C:\Users\GPedra\AppData\Local\Temp\RtmpIjVF1d/jmvbaseR_0.2.0.tar.gz" \
--as-cran --timings --no-manual

* using log directory 'C:/Users/GPedra/Desktop/jmvbaseR.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using options '--no-manual --as-cran'
* checking for file 'jmvbaseR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'jmvbaseR' version '0.2.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'jmvbaseR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
GPL3
Standardizable: FALSE
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
'jamovi'
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
'anovaBase' 'anovaClass' 'anovaResults' 'ttestISBase' 'ttestISClass'
'ttestISResults' 'ttestOneSBase' 'ttestOneSClass' 'ttestOneSResults'
'ttestPSBase' 'ttestPSClass' 'ttestPSResults'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... NONE
* DONE
Status: 1 WARNING, 2 NOTEs

checking for missing documentation entries ... WARNING
Undocumented code objects:
'anovaBase' 'anovaClass' 'anovaResults' 'ttestISBase' 'ttestISClass'
'ttestISResults' 'ttestOneSBase' 'ttestOneSClass' 'ttestOneSResults'
'ttestPSBase' 'ttestPSClass' 'ttestPSResults'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.

checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
GPL3
Standardizable: FALSE

checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
'jamovi'
R CMD check results
0 errors | 1 warning | 2 notes

R CMD check succeeded

Best regards
Giuseppe
User avatar
jonathon
Posts: 2613
Joined: Fri Jan 27, 2017 10:04 am

Re: problems with jmvtools::install() and jmvtools::create()

Post by jonathon »

wow. you have this issue on two computers! this is totally nuts.

thanks for having the patience to help me out with this.

still trying to figure it out. will come back to you soon.

with thanks
User avatar
jonathon
Posts: 2613
Joined: Fri Jan 27, 2017 10:04 am

Re: problems with jmvtools::install() and jmvtools::create()

Post by jonathon »

hi,

OK, i have another version which can produce even more debug information.

install it the usual way:

install.packages('jmvtools', repos='https://repo.jamovi.org')

but call install with the debug argument:

jmvtools::install(debug=TRUE)

thanks so much for your help

jonathon
pedrak
Posts: 16
Joined: Tue Apr 11, 2017 7:54 am

Re: problems with jmvtools::install() and jmvtools::create()

Post by pedrak »

Hi Jonathon,
I think Jamovi is a great project and really wish you every possible success with it. If I can help in some way its a pleasure for me.

Here is the new output.

> jmvtools::install(debug=TRUE)

jamovi compiler

jamovi found at C:\Program Files\jamovi 0.7.3.0 Beta 3\bin\jamovi.exe

wrote: anova.h.R
wrote: anova.src.js
wrote: anova.js
wrote: ttestis.h.R
wrote: ttestis.src.js
wrote: ttestis.js
wrote: ttestones.h.R
wrote: ttestones.src.js
wrote: ttestones.js
wrote: ttestps.h.R
wrote: ttestps.src.js
wrote: ttestps.js
writing module meta
wrote: 0000.yaml
wrote: jamovi.yaml
[Sat Apr 29 2017 09:14:39 GMT+0200 (ora legale Europa occidentale)] DEBUG checking existence of C:\Users\679408\Desktop\jmvbaseR-master\build\R
[Sat Apr 29 2017 09:14:39 GMT+0200 (ora legale Europa occidentale)] DEBUG exists
[Sat Apr 29 2017 09:14:39 GMT+0200 (ora legale Europa occidentale)] DEBUG reading dir C:\Users\679408\Desktop\jmvbaseR-master\build\R
[Sat Apr 29 2017 09:14:39 GMT+0200 (ora legale Europa occidentale)] DEBUG read
[Sat Apr 29 2017 09:14:39 GMT+0200 (ora legale Europa occidentale)] DEBUG reading DESCRIPTION
[Sat Apr 29 2017 09:14:39 GMT+0200 (ora legale Europa occidentale)] DEBUG read
[Sat Apr 29 2017 09:14:39 GMT+0200 (ora legale Europa occidentale)] DEBUG creating temp dir
[Sat Apr 29 2017 09:14:39 GMT+0200 (ora legale Europa occidentale)] DEBUG created
[Sat Apr 29 2017 09:14:39 GMT+0200 (ora legale Europa occidentale)] DEBUG copying src to temp

Error: EBUSY: resource busy or locked, read

Warning message:
running command '"C:/Users/679408/Documents/R/win-library/3.3/node/node.exe" "C:/Users/679408/Documents/R/win-library/3.3/jmvtools/node_modules/jamovi-compiler/index.js" --install "." --home "C:\Program Files\jamovi 0.7.3.0 Beta 3\bin" --debug' had status 1

------------------
I didn't tell you before, I am from in Italy. Keyboard and country settings are european (Italy).

Best regard
Giuseppe
User avatar
jonathon
Posts: 2613
Joined: Fri Jan 27, 2017 10:04 am

Re: problems with jmvtools::install() and jmvtools::create()

Post by jonathon »

OK, the issue seems to be with temporary directory stuff. we create a temporary directory, copy some things into it, and then zip it up to form the .jmo module file.

for whatever reason, the temp folder seems to be 'locked', or not ready yet, or something. its possibly a race condition, so i've added a two second delay between the creation of the temp directory, and copying stuff to it. lets see if that works.

can you try the latest jmvtools?

with thanks
pedrak
Posts: 16
Joined: Tue Apr 11, 2017 7:54 am

Re: problems with jmvtools::install() and jmvtools::create()

Post by pedrak »

sorry, still some problems
Giuseppe

jamovi compiler

jamovi found at C:\Program Files\jamovi 0.7.3.0 Beta 3\bin\jamovi.exe
wrote: anova.h.R
wrote: anova.src.js
wrote: anova.js
wrote: ttestis.h.R
wrote: ttestis.src.js
wrote: ttestis.js
wrote: ttestones.h.R
wrote: ttestones.src.js
wrote: ttestones.js
wrote: ttestps.h.R
wrote: ttestps.src.js
wrote: ttestps.js
writing module meta
wrote: 0000.yaml
wrote: jamovi.yaml
[Mon May 01 2017 16:43:07 GMT+0200 (ora legale Europa occidentale)] DEBUG checking existence of C:\Users\679408\Desktop\jmvbaseR-master\build\R
[Mon May 01 2017 16:43:07 GMT+0200 (ora legale Europa occidentale)] DEBUG exists
[Mon May 01 2017 16:43:07 GMT+0200 (ora legale Europa occidentale)] DEBUG reading dir C:\Users\679408\Desktop\jmvbaseR-master\build\R
[Mon May 01 2017 16:43:07 GMT+0200 (ora legale Europa occidentale)] DEBUG read
[Mon May 01 2017 16:43:07 GMT+0200 (ora legale Europa occidentale)] DEBUG reading DESCRIPTION
[Mon May 01 2017 16:43:07 GMT+0200 (ora legale Europa occidentale)] DEBUG read
[Mon May 01 2017 16:43:07 GMT+0200 (ora legale Europa occidentale)] DEBUG creating temp dir
[Mon May 01 2017 16:43:07 GMT+0200 (ora legale Europa occidentale)] DEBUG created
[Mon May 01 2017 16:43:07 GMT+0200 (ora legale Europa occidentale)] DEBUG sleeping
[Mon May 01 2017 16:43:09 GMT+0200 (ora legale Europa occidentale)] DEBUG awoken
[Mon May 01 2017 16:43:09 GMT+0200 (ora legale Europa occidentale)] DEBUG copying src to temp

Error: EBUSY: resource busy or locked, read

Warning message:
running command '"C:/Users/679408/Documents/R/win-library/3.3/node/node.exe" "C:/Users/679408/Documents/R/win-library/3.3/jmvtools/node_modules/jamovi-compiler/index.js" --install "." --home "C:\Program Files\jamovi 0.7.3.0 Beta 3\bin" --debug' had status 1
User avatar
jonathon
Posts: 2613
Joined: Fri Jan 27, 2017 10:04 am

Re: problems with jmvtools::install() and jmvtools::create()

Post by jonathon »

OK! i still have zero idea why this is happening *BUT* i think if you try the latest version of jmvtools it will solve the issue! :)

thanks so much for your perseverance!

jonathon
pedrak
Posts: 16
Joined: Tue Apr 11, 2017 7:54 am

Re: problems with jmvtools::install() and jmvtools::create()

Post by pedrak »

Got it !!
----------------

jamovi compiler

jamovi found at C:\Program Files\jamovi 0.7.3.0 Beta 3\bin\jamovi.exe

wrote: anova.h.R
wrote: anova.src.js
wrote: anova.js
wrote: ttestis.h.R
wrote: ttestis.src.js
wrote: ttestis.js
wrote: ttestones.h.R
wrote: ttestones.src.js
wrote: ttestones.js
wrote: ttestps.h.R
wrote: ttestps.src.js
wrote: ttestps.js
writing module meta
wrote: 0000.yaml
wrote: jamovi.yaml
* installing *source* package 'jmvbaseR' ...
Warning in as.POSIXlt.POSIXct(x, tz) : unknown timezone 'Europe/Berlin'
Warning in as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
Warning in as.POSIXlt.POSIXct(x, tz) :
unknown timezone 'America/New_York'
Warning in as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
Warning in as.POSIXlt.POSIXct(x, tz) :
unknown timezone 'America/New_York'
** R
** preparing package for lazy loading
** help
*** installing help indices
Warning in file.copy(file.path(R.home("doc"), "html", "R.css"), outman) :
problem copying C:\PROGRA~1\JAMOVI~1.0B~\FRAMEW~1\R\doc\html\R.css to C:\Users\GPedra\Desktop\jmvbaseR-master\build\R\jmvbaseR\html\R.css: No such file or directory
** building package indices
** testing if installed package can be loaded
* DONE (jmvbaseR)
wrote module: jmvbaseR.jmo

Installing jmvbaseR.jmo

Module installed successfully

Great work, thanks !!

Best regards
Giuseppe
User avatar
jonathon
Posts: 2613
Joined: Fri Jan 27, 2017 10:04 am

Re: problems with jmvtools::install() and jmvtools::create()

Post by jonathon »

oh man, i'm so relieved :)

thanks again!

jonathon
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