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Unable to Install Program #60
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Hello,
For a Mac installation it is normal for the following step to fail, but it will get the correct packages installed.
install_github("nclark-lab/RERconverge", dependencies = T
Then you should download the binary and instal with this command:
R CMD INSTALL Mac.RERconverge_0.2.0.tgz
Those instructions in more detail are here:
https://github.com/nclark-lab/RERconverge/wiki/Binary
Let me know if those steps work for you.
Best,
-Nathan
…_____________________________
Nathan Clark
Associate Professor of Human Genetics
Adjunct Professor of Computational and Systems Biology
University of Utah
nclark@utah.edu<mailto:nclark@utah.edu>
http://nclarklab.org/
On Feb 15, 2021, at 9:03 AM, andypaige772 <notifications@github.com<mailto:notifications@github.com>> wrote:
Dear Developers,
I am having trouble installing RERconverge.
First, I tried installing the program on my Mac with Catalina. I downloaded the binary file in the terminal according to the wiki. But after library(devtools) and install_github("nclark-lab/RERconverge", dependencies = T), and selected to have all the packages updated. I received an error message that there was a "non-zero exit status".
I updated to Big Sur and tried installing clang8 (64-bit) and gfortran (4.2.3) and the latest xcode for mac. I am now getting
Downloading GitHub repo nclark-lab/RERconverge@Head
Error: Failed to install 'RERconverge' from GitHub:
Could not find tools necessary to compile a package
Call 'pkgbuild::check_build_tools(debug = TRUE_' to diagnose the problem.
I receive a window that says "Install Build Tools" Building R package from source requires installation of additional build tools. Do you want to install the additional tools now?
I select "Yes" but it doesn't resolve the issue.
I have also tried installing RERconverge using Windows 10 on a PC. with the following:
library(devtools)
Loading required package: usethis
install_github("nclark-lab/RERconverge", dependencies = TRUE)
Downloading GitHub repo nclark-lab/RERconverge@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: rlang (0.4.9 -> 0.4.10 ) [CRAN]
5: digest (0.6.25 -> 0.6.27 ) [CRAN]
6: fansi (0.4.1 -> 0.4.2 ) [CRAN]
7: crayon (1.3.4 -> 1.4.1 ) [CRAN]
8: cli (2.2.0 -> 2.3.0 ) [CRAN]
9: tibble (3.0.4 -> 3.0.6 ) [CRAN]
10: withr (2.3.0 -> 2.4.1 ) [CRAN]
11: waldo (0.2.3 -> 0.2.4 ) [CRAN]
12: brio (1.1.0 -> 1.1.1 ) [CRAN]
13: testthat (3.0.1 -> 3.0.2 ) [CRAN]
14: backports (1.1.9 -> 1.2.1 ) [CRAN]
15: cpp11 (0.2.4 -> 0.2.6 ) [CRAN]
16: Rcpp (1.0.5 -> 1.0.6 ) [CRAN]
17: dplyr (1.0.2 -> 1.0.4 ) [CRAN]
18: broom (0.7.3 -> 0.7.4 ) [CRAN]
19: mime (0.9 -> 0.10 ) [CRAN]
20: xfun (0.17 -> 0.21 ) [CRAN]
21: knitr (1.30 -> 1.31 ) [CRAN]
22: htmltools (0.5.0 -> 0.5.1.1 ) [CRAN]
23: plotrix (3.7-8 -> 3.8-1 ) [CRAN]
24: expm (0.999-5 -> 0.999-6 ) [CRAN]
25: mice (3.12.0 -> 3.13.0 ) [CRAN]
26: caTools (1.18.0 -> 1.18.1 ) [CRAN]
27: RcppArmad... (0.10.1.2.0 -> 0.10.2.1.0) [CRAN]
Enter one or more numbers, or an empty line to skip updates:1
rlang (0.4.9 -> 0.4.10 ) [CRAN]
digest (0.6.25 -> 0.6.27 ) [CRAN]
fansi (0.4.1 -> 0.4.2 ) [CRAN]
crayon (1.3.4 -> 1.4.1 ) [CRAN]
cli (2.2.0 -> 2.3.0 ) [CRAN]
tibble (3.0.4 -> 3.0.6 ) [CRAN]
withr (2.3.0 -> 2.4.1 ) [CRAN]
waldo (0.2.3 -> 0.2.4 ) [CRAN]
brio (1.1.0 -> 1.1.1 ) [CRAN]
testthat (3.0.1 -> 3.0.2 ) [CRAN]
backports (1.1.9 -> 1.2.1 ) [CRAN]
cpp11 (0.2.4 -> 0.2.6 ) [CRAN]
Rcpp (1.0.5 -> 1.0.6 ) [CRAN]
dplyr (1.0.2 -> 1.0.4 ) [CRAN]
broom (0.7.3 -> 0.7.4 ) [CRAN]
mime (0.9 -> 0.10 ) [CRAN]
xfun (0.17 -> 0.21 ) [CRAN]
knitr (1.30 -> 1.31 ) [CRAN]
htmltools (0.5.0 -> 0.5.1.1 ) [CRAN]
plotrix (3.7-8 -> 3.8-1 ) [CRAN]
expm (0.999-5 -> 0.999-6 ) [CRAN]
mice (3.12.0 -> 3.13.0 ) [CRAN]
caTools (1.18.0 -> 1.18.1 ) [CRAN]
RcppArmad... (0.10.1.2.0 -> 0.10.2.1.0) [CRAN]
Installing 24 packages: rlang, digest, fansi, crayon, cli, tibble, withr, waldo, brio, testthat, backports, cpp11, Rcpp, dplyr, broom, mime, xfun, knitr, htmltools, plotrix, expm, mice, caTools, RcppArmadillo
Installing packages into ‘C:/Users/andyp/OneDrive/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
There are binary versions available but the source versions are
later:
binary source needs_compilation
crayon 1.4.0 1.4.1 FALSE
waldo 0.2.3 0.2.4 FALSE
testthat 3.0.1 3.0.2 TRUE
mime 0.9 0.10 TRUE
xfun 0.20 0.21 TRUE
RcppArmadillo 0.10.1.2.2 0.10.2.1.0 TRUE
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/rlang_0.4.10.zip'
Content type 'application/zip' length 1196950 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/digest_0.6.27.zip'
Content type 'application/zip' length 268490 bytes (262 KB)
downloaded 262 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/fansi_0.4.2.zip'
Content type 'application/zip' length 223895 bytes (218 KB)
downloaded 218 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/cli_2.3.0.zip'
Content type 'application/zip' length 474483 bytes (463 KB)
downloaded 463 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/tibble_3.0.6.zip'
Content type 'application/zip' length 836444 bytes (816 KB)
downloaded 816 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/withr_2.4.1.zip'
Content type 'application/zip' length 206067 bytes (201 KB)
downloaded 201 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/brio_1.1.1.zip'
Content type 'application/zip' length 45687 bytes (44 KB)
downloaded 44 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/backports_1.2.1.zip'
Content type 'application/zip' length 98506 bytes (96 KB)
downloaded 96 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/cpp11_0.2.6.zip'
Content type 'application/zip' length 222568 bytes (217 KB)
downloaded 217 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/Rcpp_1.0.6.zip'
Content type 'application/zip' length 3253235 bytes (3.1 MB)
downloaded 3.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/dplyr_1.0.4.zip'
Content type 'application/zip' length 1329695 bytes (1.3 MB)
downloaded 1.3 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/broom_0.7.4.zip'
Content type 'application/zip' length 1789286 bytes (1.7 MB)
downloaded 1.7 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/knitr_1.31.zip'
Content type 'application/zip' length 1445881 bytes (1.4 MB)
downloaded 1.4 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/htmltools_0.5.1.1.zip'
Content type 'application/zip' length 243817 bytes (238 KB)
downloaded 238 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/plotrix_3.8-1.zip'
Content type 'application/zip' length 1138351 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/expm_0.999-6.zip'
Content type 'application/zip' length 239058 bytes (233 KB)
downloaded 233 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/mice_3.13.0.zip'
Content type 'application/zip' length 2025145 bytes (1.9 MB)
downloaded 1.9 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/caTools_1.18.1.zip'
Content type 'application/zip' length 317355 bytes (309 KB)
downloaded 309 KB
package ‘rlang’ successfully unpacked and MD5 sums checked
Error: Failed to install 'RERconverge' from GitHub:
(converted from warning) cannot remove prior installation of package ‘rlang’
What is the best way to begin to resolve the issue and install the program?
Thank you for your help.
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|
Could you try to install the attached binary file? I have tried this one on Catalina 10.15 & R 4.0.2. Let me know if new problems occur.
|
Sorry for the late response. I am currently setting up the Big Sur in the virtual environment and test RERconverge installation. I will get back to you when it's done. |
Please follow the updated guidance |
Hi Wayne and Maria,
There were 3 different webpages about installation and it was confusing. I combined them into one and deleted the two others. The information you edited 2 days ago is not lost. It's in the consolidated page here: https://github.com/nclark-lab/RERconverge/wiki/Install
The link to download the binary is broken. Under “Mac” Step 3, it gives: https://github.com/wgmao/RERconverge/tree/master/OS
Could you correct that link?
Should it be this one? https://github.com/nclark-lab/RERconverge/releases
Thanks,
-Nathan
…_____________________________
Nathan Clark
Associate Professor of Human Genetics
Adjunct Professor of Computational and Systems Biology
University of Utah
nclark@utah.edu<mailto:nclark@utah.edu>
http://nclarklab.org/
On Feb 25, 2021, at 2:31 PM, wgmao <notifications@github.com<mailto:notifications@github.com>> wrote:
Please follow the updated guidance https://github.com/nclark-lab/RERconverge/wiki/Github and try to install from the source. I have successfully installed on Big Sur with gfortran 10.2 for Big Sur (macOS 11), for Intel processors. You may have M1 processors so you need to select the right gfortran installation file accordingly.
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|
Great. Thanks Wayne for updating it and the navigation bar.
-Nathan
On Feb 28, 2021, at 12:24 PM, wgmao <notifications@github.com> wrote:
* The navigation bar of the wiki page has been updated accordingly. Thank you for merging the instructions.
* You're right. The link has been updated.
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Sorry for late reply. I think you are pretty close to getting it done. You don't need to install binary before installing from GitHub. I would suggest the following steps to resolve your problems.
|
Could you uninstall the RERconverge and install from the following binary file? If it works, you can ignore the following instruction. If this doesn't work, we have to install from the source. First could you type |
Dear Developers,
I am having trouble installing RERconverge.
First, I tried installing the program on my Mac with Catalina. I downloaded the binary file in the terminal according to the wiki. But after library(devtools) and install_github("nclark-lab/RERconverge", dependencies = T), and selected to have all the packages updated. I received an error message that there was a "non-zero exit status".
I updated to Big Sur and tried installing clang8 (64-bit) and gfortran (4.2.3) and the latest xcode for mac. I am now getting
Downloading GitHub repo nclark-lab/RERconverge@Head
Error: Failed to install 'RERconverge' from GitHub:
Could not find tools necessary to compile a package
Call 'pkgbuild::check_build_tools(debug = TRUE_' to diagnose the problem.
I receive a window that says "Install Build Tools" Building R package from source requires installation of additional build tools. Do you want to install the additional tools now?
I select "Yes" but it doesn't resolve the issue.
I have also tried installing RERconverge using Windows 10 on a PC. with the following:
library(devtools)
Loading required package: usethis
1: All
2: CRAN packages only
3: None
4: rlang (0.4.9 -> 0.4.10 ) [CRAN]
5: digest (0.6.25 -> 0.6.27 ) [CRAN]
6: fansi (0.4.1 -> 0.4.2 ) [CRAN]
7: crayon (1.3.4 -> 1.4.1 ) [CRAN]
8: cli (2.2.0 -> 2.3.0 ) [CRAN]
9: tibble (3.0.4 -> 3.0.6 ) [CRAN]
10: withr (2.3.0 -> 2.4.1 ) [CRAN]
11: waldo (0.2.3 -> 0.2.4 ) [CRAN]
12: brio (1.1.0 -> 1.1.1 ) [CRAN]
13: testthat (3.0.1 -> 3.0.2 ) [CRAN]
14: backports (1.1.9 -> 1.2.1 ) [CRAN]
15: cpp11 (0.2.4 -> 0.2.6 ) [CRAN]
16: Rcpp (1.0.5 -> 1.0.6 ) [CRAN]
17: dplyr (1.0.2 -> 1.0.4 ) [CRAN]
18: broom (0.7.3 -> 0.7.4 ) [CRAN]
19: mime (0.9 -> 0.10 ) [CRAN]
20: xfun (0.17 -> 0.21 ) [CRAN]
21: knitr (1.30 -> 1.31 ) [CRAN]
22: htmltools (0.5.0 -> 0.5.1.1 ) [CRAN]
23: plotrix (3.7-8 -> 3.8-1 ) [CRAN]
24: expm (0.999-5 -> 0.999-6 ) [CRAN]
25: mice (3.12.0 -> 3.13.0 ) [CRAN]
26: caTools (1.18.0 -> 1.18.1 ) [CRAN]
27: RcppArmad... (0.10.1.2.0 -> 0.10.2.1.0) [CRAN]
Enter one or more numbers, or an empty line to skip updates:1
rlang (0.4.9 -> 0.4.10 ) [CRAN]
digest (0.6.25 -> 0.6.27 ) [CRAN]
fansi (0.4.1 -> 0.4.2 ) [CRAN]
crayon (1.3.4 -> 1.4.1 ) [CRAN]
cli (2.2.0 -> 2.3.0 ) [CRAN]
tibble (3.0.4 -> 3.0.6 ) [CRAN]
withr (2.3.0 -> 2.4.1 ) [CRAN]
waldo (0.2.3 -> 0.2.4 ) [CRAN]
brio (1.1.0 -> 1.1.1 ) [CRAN]
testthat (3.0.1 -> 3.0.2 ) [CRAN]
backports (1.1.9 -> 1.2.1 ) [CRAN]
cpp11 (0.2.4 -> 0.2.6 ) [CRAN]
Rcpp (1.0.5 -> 1.0.6 ) [CRAN]
dplyr (1.0.2 -> 1.0.4 ) [CRAN]
broom (0.7.3 -> 0.7.4 ) [CRAN]
mime (0.9 -> 0.10 ) [CRAN]
xfun (0.17 -> 0.21 ) [CRAN]
knitr (1.30 -> 1.31 ) [CRAN]
htmltools (0.5.0 -> 0.5.1.1 ) [CRAN]
plotrix (3.7-8 -> 3.8-1 ) [CRAN]
expm (0.999-5 -> 0.999-6 ) [CRAN]
mice (3.12.0 -> 3.13.0 ) [CRAN]
caTools (1.18.0 -> 1.18.1 ) [CRAN]
RcppArmad... (0.10.1.2.0 -> 0.10.2.1.0) [CRAN]
Installing 24 packages: rlang, digest, fansi, crayon, cli, tibble, withr, waldo, brio, testthat, backports, cpp11, Rcpp, dplyr, broom, mime, xfun, knitr, htmltools, plotrix, expm, mice, caTools, RcppArmadillo
Installing packages into ‘C:/Users/andyp/OneDrive/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
There are binary versions available but the source versions are
later:
binary source needs_compilation
crayon 1.4.0 1.4.1 FALSE
waldo 0.2.3 0.2.4 FALSE
testthat 3.0.1 3.0.2 TRUE
mime 0.9 0.10 TRUE
xfun 0.20 0.21 TRUE
RcppArmadillo 0.10.1.2.2 0.10.2.1.0 TRUE
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/rlang_0.4.10.zip'
Content type 'application/zip' length 1196950 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/digest_0.6.27.zip'
Content type 'application/zip' length 268490 bytes (262 KB)
downloaded 262 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/fansi_0.4.2.zip'
Content type 'application/zip' length 223895 bytes (218 KB)
downloaded 218 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/cli_2.3.0.zip'
Content type 'application/zip' length 474483 bytes (463 KB)
downloaded 463 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/tibble_3.0.6.zip'
Content type 'application/zip' length 836444 bytes (816 KB)
downloaded 816 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/withr_2.4.1.zip'
Content type 'application/zip' length 206067 bytes (201 KB)
downloaded 201 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/brio_1.1.1.zip'
Content type 'application/zip' length 45687 bytes (44 KB)
downloaded 44 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/backports_1.2.1.zip'
Content type 'application/zip' length 98506 bytes (96 KB)
downloaded 96 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/cpp11_0.2.6.zip'
Content type 'application/zip' length 222568 bytes (217 KB)
downloaded 217 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/Rcpp_1.0.6.zip'
Content type 'application/zip' length 3253235 bytes (3.1 MB)
downloaded 3.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/dplyr_1.0.4.zip'
Content type 'application/zip' length 1329695 bytes (1.3 MB)
downloaded 1.3 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/broom_0.7.4.zip'
Content type 'application/zip' length 1789286 bytes (1.7 MB)
downloaded 1.7 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/knitr_1.31.zip'
Content type 'application/zip' length 1445881 bytes (1.4 MB)
downloaded 1.4 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/htmltools_0.5.1.1.zip'
Content type 'application/zip' length 243817 bytes (238 KB)
downloaded 238 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/plotrix_3.8-1.zip'
Content type 'application/zip' length 1138351 bytes (1.1 MB)
downloaded 1.1 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/expm_0.999-6.zip'
Content type 'application/zip' length 239058 bytes (233 KB)
downloaded 233 KB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/mice_3.13.0.zip'
Content type 'application/zip' length 2025145 bytes (1.9 MB)
downloaded 1.9 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/caTools_1.18.1.zip'
Content type 'application/zip' length 317355 bytes (309 KB)
downloaded 309 KB
package ‘rlang’ successfully unpacked and MD5 sums checked
Error: Failed to install 'RERconverge' from GitHub:
(converted from warning) cannot remove prior installation of package ‘rlang’
What is the best way to begin to resolve the issue and install the program?
Thank you for your help.
The text was updated successfully, but these errors were encountered: