Replies: 13 comments 13 replies
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Something with build tools isn’t right. Are you running this in Rmarkdown? I’d like to see the error message under stderr |
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Thanks Kyle. Hope you and your family are doing well.
I am running this in regular R/Rstudio, not Rmarkdown. What I pasted was the whole error message from the console. There is nothing additional below stderr.
Best regards,
Suresh Agarwal
On Jul 10, 2021, at 6:16 PM, Kyle Baron ***@***.***> wrote:
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Something with build tools isn’t right. Are you running this in Rmarkdown? I’d like to see the error message under stderr
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Ok; Did you install install Rtools? What is the output of Sys.which("make")
sessionInfo()
pkgbuild::find_rtools()
pkgbuild::check_build_tools()
Sys.getenv("PATH") |
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Yes, I installed Rtools. Here is the requested output. Thanks.
Sys.which("make")
make
"c:\\Rtools\\bin\\make.exe"
sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pkgbuild_1.2.0 ubiquity_1.0.5 forcats_0.5.1 stringr_1.4.0
[5] dplyr_1.0.5 purrr_0.3.4 readr_1.4.0 tidyr_1.1.3
[9] tibble_3.1.0 ggplot2_3.3.3 tidyverse_1.3.0 mrgsolve_0.11.1
loaded via a namespace (and not attached):
[1] nlme_3.1-152 fs_1.5.0 lubridate_1.7.10
[4] doParallel_1.0.16 httr_1.4.2 numDeriv_2016.8-1.1
[7] tools_4.0.5 backports_1.2.1 utf8_1.2.1
[10] R6_2.5.0 DBI_1.1.1 colorspace_2.0-0
[13] withr_2.4.1 prettyunits_1.1.1 processx_3.5.1
[16] tidyselect_1.1.0 gridExtra_2.3 compiler_4.0.5
[19] cli_2.4.0 rvest_1.0.0 flextable_0.6.6
[22] xml2_1.3.2 officer_0.3.18 rhandsontable_0.3.8
[25] scales_1.1.1 callr_3.6.0 systemfonts_1.0.2
[28] digest_0.6.27 rmarkdown_2.7 base64enc_0.1-3
[31] pkgconfig_2.0.3 htmltools_0.5.1.1 dbplyr_2.1.1
[34] fastmap_1.1.0 htmlwidgets_1.5.3 rlang_0.4.10
[37] readxl_1.3.1 rstudioapi_0.13 shiny_1.6.0
[40] generics_0.1.0 jsonlite_1.7.2 zip_2.1.1
[43] magrittr_2.0.1 Rcpp_1.0.6 munsell_0.5.0
[46] fansi_0.4.2 gdtools_0.2.3 lifecycle_1.0.0
[49] stringi_1.5.3 MASS_7.3-53.1 grid_4.0.5
[52] parallel_4.0.5 promises_1.2.0.1 crayon_1.4.1
[55] lattice_0.20-41 haven_2.3.1 hms_1.0.0
[58] ps_1.6.0 knitr_1.32 pillar_1.6.0
[61] uuid_0.1-4 pso_1.0.3 codetools_0.2-18
[64] reprex_2.0.0 glue_1.4.2 evaluate_0.14
[67] data.table_1.14.0 modelr_0.1.8 deSolve_1.28
[70] vctrs_0.3.7 httpuv_1.6.1 foreach_1.5.1
[73] cellranger_1.1.0 gtable_0.3.0 assertthat_0.2.1
[76] xfun_0.22 mime_0.10 xtable_1.8-4
[79] broom_0.7.6 later_1.2.0 PKNCA_0.9.4
[82] optimx_2021-6.12 iterators_1.0.13 tinytex_0.31
[85] ellipsis_0.3.1
pkgbuild::find_rtools()
[1] TRUE
pkgbuild::check_build_tools()
Your system is ready to build packages!
Sys.getenv("PATH")
[1] "c:/Rtools/bin;C:\\Users\\su904624\\OneDrive - BioMarin\\Documents\\R\\R-4.0.5\\bin\\x64;C:\\Program Files (x86)\\Certara\\Phoenix\\application\\lib\\NLME\\Executables\\;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files (x86)\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Program Files\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Users\\su904624\\AppData\\Local\\Microsoft\\WindowsApps;"
From: Kyle Baron ***@***.***>
Sent: Monday, July 12, 2021 6:32 AM
To: metrumresearchgroup/mrgsolve ***@***.***>
Cc: Suresh Agarwal ***@***.***>; Author ***@***.***>
Subject: Re: [metrumresearchgroup/mrgsolve] Error: the model build step failed (#846)
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Ok; Did you install install Rtools? What is the output of
Sys.which("make")
sessionInfo()
pkgbuild::find_rtools()
pkgbuild::check_build_tools()
Sys.getenv("PATH")
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It looks like it is set up correctly but until we see that error message, there isn't a lot I can do. One thing you could try is: mod <- mread("pk2", modlib(), ignore.stdout = FALSE)and see what comes out of that. |
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The first part of the output below doesn't look right. What do you think?
[1] "c:/Rtools/bin;C:\Users\su904624\OneDrive - BioMarin\Documents\R\R-4.0.5\bin\x64;C:\Program Files (x86)\Certara\Phoenix\application\lib\NLME\Executables\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Users\su904624\AppData\Local\Microsoft\WindowsApps;" |
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Ok; What do you think it should say? I'm assuming that you checked What do you have for R.home()
tempdir() |
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c:/Rtools/bin is correct. |
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Ok; here is the output-
… mod <- mread("pk2", modlib(), ignore.stdout = FALSE)
---:: stdout ::---------------------------------------------
---:: stderr ::---------------------------------------------
------------------------------------------------------------
Error: the model build step failed.
From: Kyle Baron ***@***.***>
Sent: Monday, July 12, 2021 8:19 AM
To: metrumresearchgroup/mrgsolve ***@***.***>
Cc: Suresh Agarwal ***@***.***>; Author ***@***.***>
Subject: Re: [metrumresearchgroup/mrgsolve] Error: the model build step failed (#846)
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It looks like it is set up correctly but until we see that error message, there isn't a lot I can do. One thing you could try is:
mod <- mread("pk2", modlib(), ignore.stdout = FALSE)
and see what comes out of that.
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R.home()
[1] "C:/Users/su904624/ONEDRI~1/DOCUME~1/R/R-40~1.5"
tempdir()
[1] "C:\\Users\\su904624\\AppData\\Local\\Temp\\RtmpO8ujNS"
From: Kyle Baron ***@***.***>
Sent: Monday, July 12, 2021 8:31 AM
To: metrumresearchgroup/mrgsolve ***@***.***>
Cc: Suresh Agarwal ***@***.***>; Author ***@***.***>
Subject: Re: [metrumresearchgroup/mrgsolve] Error: the model build step failed (#846)
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Ok; What do you think it should say? I'm assuming that you checked c:/Rtools/bin and that is correct. I don't know where your home directory is or if you're working in OneDrive or not. I'd make sure your R installation and everything you do is local on your computer. But I have no clue why you aren't seeing any content from stdout or stderr so it makes me think something is going wrong there.
What do you have for
R.home()
tempdir()
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Not sure what else I can do. We do need those error messages to figure out what is the problem. I've never had this information not coming out on the console when running plain old R code (not Rmarkdown as you mentioned). You might also run the code from the command line R just to make sure Rstudio isn't misbehaving. I can go back to my windows machine and verify the behavior but I don't see a reason why messages would just not show up like this with regular R code in an R file. Please keep me posted if any other information becomes available or if somehow you start seeing those error messages and I'd be happy to dig back into it with you. |
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I ran it on the command line R and still get the exact same error confirming RStudio is not misbehaving. I will keep you posted if any other info becomes available or error messages start showing up.
From: Kyle Baron ***@***.***>
Sent: Monday, July 12, 2021 12:07 PM
To: metrumresearchgroup/mrgsolve ***@***.***>
Cc: Suresh Agarwal ***@***.***>; Author ***@***.***>
Subject: Re: [metrumresearchgroup/mrgsolve] Error: the model build step failed (#846)
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Not sure what else I can do. We do need those error messages to figure out what is the problem. I've never had this information not coming out on the console when running plain old R code (not Rmarkdown as you mentioned). You might also run the code from the command line R just to make sure Rstudio isn't misbehaving. I can go back to my windows machine and verify the behavior but I don't see a reason why messages would just not show up like this with regular R code in an R file. Please keep me posted if any other information becomes available or if somehow you start seeing those error messages and I'd be happy to dig back into it with you.
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Here's another idea: Run this and then navigate into the total 32
-rw-r--r-- 1 kyleb staff 645B Jul 12 14:19 error-mread-header.h
-rw-r--r-- 1 kyleb staff 311B Jul 12 14:19 error-mread-source.cpp
-rw-r--r-- 1 kyleb staff 146B Jul 12 14:19 system4__stderr__error
-rw-r--r-- 1 kyleb staff 325B Jul 12 14:19 system4__stdout__errorCode: library(mrgsolve)
code <- '
[ main ]
double a = 1
'
mod <- mcode("error", code, soloc = 'err') |
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Still same.
library(mrgsolve)
code <- '
+ [ main ]
+ double a = 1
+
+ '
mod <- mcode("error", code, soloc = 'err')
Creating build directory: err
Building error ... error.
---:: stderr ::---------------------------------------------
------------------------------------------------------------
Error: the model build step failed.
From: Kyle Baron ***@***.***>
Sent: Monday, July 12, 2021 12:22 PM
To: metrumresearchgroup/mrgsolve ***@***.***>
Cc: Suresh Agarwal ***@***.***>; Author ***@***.***>
Subject: Re: [metrumresearchgroup/mrgsolve] Error: the model build step failed (#846)
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.
Here's another idea: Run this and then navigate into the err directory until you see these files. That might be informative.
total 32
…-rw-r--r-- 1 kyleb staff 645B Jul 12 14:19 error-mread-header.h
-rw-r--r-- 1 kyleb staff 311B Jul 12 14:19 error-mread-source.cpp
-rw-r--r-- 1 kyleb staff 146B Jul 12 14:19 system4__stderr__error
-rw-r--r-- 1 kyleb staff 325B Jul 12 14:19 system4__stdout__error
Code:
library(mrgsolve)
code <- '
[ main ]
double a = 1
'
mod <- mcode("error", code, soloc = 'err')
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Did you find the files there? That was the point of that exercise. |
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We want these files: |
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Yes, I see those files in the error folder but they are empty.
From: Kyle Baron ***@***.***>
Sent: Monday, July 12, 2021 12:27 PM
To: metrumresearchgroup/mrgsolve ***@***.***>
Cc: Suresh Agarwal ***@***.***>; Author ***@***.***>
Subject: Re: [metrumresearchgroup/mrgsolve] Error: the model build step failed (#846)
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We want these files:
…-rw-r--r-- 1 kyleb staff 146B Jul 12 14:19 system4__stderr__error
-rw-r--r-- 1 kyleb staff 325B Jul 12 14:19 system4__stdout__error
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Hi @agar0152 and @kylebaron I could be wrong, and I often am (part of being a developer I suppose), I think the problem is that your home directory is in a network directory, specifically OneDrive. At Novartis the Rtools doesn't work well when the home drive is linked to OneDrive. For https://github.com/nlmixrdevelopment/nlmixr/blob/master/build/installation-notes.rtf |
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From the nlmixr install notes: nlmixr and $HOME directoriesBased on organizations and your name you may have either a network drive attached to your home directory or have international characters in your name. Either can be problematic for R and for certain R packages nlmixr interacts with. To be safe a My guess this is needed for the excellent |
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It looks like R itself is installed under OneDrive - will that cause a problem too? |
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Yes. That will cause a problem as well. When I first started at Novartis, people tried to install to their home drive. The access control for windows often do not allow loading binaries (like dlls) from network locations because of the possibility of viruses. This is problematic for any high performance computing package. I also have people install R into a user writable directory. The nlmixr installer would install in the APPDATA directory or the c:\R\ directory to overcome this limitation. International characters also don't work with windows R very well (though they are trying to remedy that) |
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Sorry for the delayed reply. I will work on this and report back how it went.
From: Matthew Fidler ***@***.***>
Sent: Monday, July 12, 2021 12:49 PM
To: metrumresearchgroup/mrgsolve ***@***.***>
Cc: Suresh Agarwal ***@***.***>; Mention ***@***.***>
Subject: Re: [metrumresearchgroup/mrgsolve] Error: the model build step failed (#846)
CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.
Yes. That will cause a problem as well. When I first started people tried to install to their home drive. The access control for windows often do not allow loading binaries (like dlls) from network locations because of the possibility of viruses.
I also have people install R into a user writable directory. The nlmixr installer would install in the APPDATA directory or the c:\R\ directory to overcome this limitation. International characters also don't work with windows R very well (though they are trying to remedy that)
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I installed R on the local machine. Here is the output for Sys.getenv("PATH") Since RTools is not in the path, I tried to edit the .Renviron file using the command file.edit("~/.Renviron") but I am not seeing a window to add the PATH. Any ideas how to get RTools in the path above? |
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I am unsure what you mean by the window to add to the path. One way to make sure that it is setup correctly is to overwrite what you may already have: writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"',"~/.Renviron")Then you should be able to restart R and have Rtools in the correct place in the path |
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Thanks Matt. I meant to say a separate Tab was not popping up to add the path. I think it’s related to not having admin rights. When I tried to run the code you provided, I am seeing this permission denied error. I contacted our IT to get admin rights and tried running it again and still getting the same error.
Error in file(con, "w") : cannot open the connection
In addition: Warning message:
In file(con, "w") : cannot open file 'C:/.Renviron': Permission denied
I tried to copy paste the .Renviron file from my one-drive Rinstall and was able to get Rtools added in the path as shown below. However, still getting the same build error.
Sys.getenv("PATH")
[1] "c:/Rtools/bin;C:\\R-4.1.0\\bin\\x64;C:\\Program Files (x86)\\Certara\\Phoenix\\application\\lib\\NLME\\Executables\\;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\System32\\Wbem;C:\\WINDOWS\\System32\\WindowsPowerShell\\v1.0\\;C:\\Program Files (x86)\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Program Files\\Intel\\Intel(R) Management Engine Components\\DAL;C:\\Users\\su904624\\AppData\\Local\\Microsoft\\WindowsApps;"
From: Matthew Fidler ***@***.***>
Sent: Wednesday, July 14, 2021 1:04 PM
To: metrumresearchgroup/mrgsolve ***@***.***>
Cc: Suresh Agarwal ***@***.***>; Mention ***@***.***>
Subject: Re: [metrumresearchgroup/mrgsolve] Error: the model build step failed (#846)
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I am unsure what you mean by the window to add to the path.
One way to make sure that it is setup correctly is to overwrite what you may already have:
writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"',"~/.Renviron")
Then you should be able to restart R and have Rtools in the correct place in the path
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My guess is the My suggestion is to create a directory I am unsure what is write protected on your computer. Let me know if this works for you. |
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I am getting the model build step failed error. Using other threads, I tried a few things but still getting the same error. I don't have admin rights as I am on company laptop.
---:: stderr ::---------------------------------------------
Error: the model build step failed.
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