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Unable to Install Program #60

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andypaige772 opened this issue Feb 15, 2021 · 13 comments
Open

Unable to Install Program #60

andypaige772 opened this issue Feb 15, 2021 · 13 comments

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@andypaige772
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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.
@nclark-lab
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nclark-lab commented Feb 15, 2021 via email

@andypaige772
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Hi Nathan,
I tried the following:

library(devtools)
Loading required package: usethis

Received the same message regarding Installing Build Tools (clicked Yes).

Then did the following:

install_github("nclark-lab/RERconverge", dependencies = T)
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 downloaded the binary file and installed with the following in the terminal (R CMD INSTALL Mac.RERconverge_0.2.0.tgz. I received a message *DONE (RERconverge)
Screen Shot 2021-02-17 at 4 14 07 PM

Then I tried library(RERconverge) and received the following errors:

library(RERconverge)
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

lowess

Loading required package: phytools
Loading required package: ape
Loading required package: maps
Loading required package: geiger
Loading required package: knitr
Loading required package: Rcpp
Loading required package: RcppArmadillo
Loading required package: weights
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2
Registered S3 method overwritten by 'htmlwidgets':
method from
print.htmlwidget tools:rstudio
Registered S3 method overwritten by 'data.table':
method from
print.data.table

Attaching package: ‘Hmisc’

The following object is masked from ‘package:ape’:

zoom

The following objects are masked from ‘package:base’:

format.pval, units

Loading required package: gdata
Registered S3 method overwritten by 'gdata':
method from
reorder.factor gplots
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: ‘gdata’

The following object is masked from ‘package:gplots’:

reorder.factor

The following object is masked from ‘package:stats’:

nobs

The following object is masked from ‘package:utils’:

object.size

The following object is masked from ‘package:base’:

startsWith

Loading required package: mice

Attaching package: ‘mice’

The following object is masked from ‘package:stats’:

filter

The following objects are masked from ‘package:base’:

cbind, rbind

Loading required package: phangorn
Loading required package: dplyr

Attaching package: ‘dplyr’

The following objects are masked from ‘package:gdata’:

combine, first, last

The following objects are masked from ‘package:Hmisc’:

src, summarize

The following objects are masked from ‘package:stats’:

filter, lag

The following objects are masked from ‘package:base’:

intersect, setdiff, setequal, union

Error: package or namespace load failed for ‘RERconverge’:
package ‘RERconverge’ was installed before R 4.0.0: please re-install it

Thank you for your help!

Best,

Andy

@wgmao
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wgmao commented Feb 18, 2021

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.

  1. Unzip the file to get RERconverge_0.1.0.tgz
  2. R CMD INSTALL RERconverge_0.1.0.tgz
    RERconverge_0.1.0.tgz.zip

@andypaige772
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I unzipped the file to get RERconverge_0.1.0.tgz and installed using R CMD INSTALL RERconverge_0.1.0.tgz (I am using Big Sur Version 11.2.1, with RStudio version 1.4.1103)
Screen Shot 2021-02-19 at 2 15 36 PM

In RStudio I did library(RERconverge) and received the following:

library(RERconverge)
Loading required package: RColorBrewer
Loading required package: gplots

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

lowess

Loading required package: phytools
Loading required package: ape
Loading required package: maps
Loading required package: geiger
Loading required package: knitr
Loading required package: Rcpp
Loading required package: RcppArmadillo
Loading required package: weights
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

The following object is masked from ‘package:ape’:

zoom

The following objects are masked from ‘package:base’:

format.pval, units

Loading required package: gdata
Registered S3 method overwritten by 'gdata':
method from
reorder.factor gplots
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: ‘gdata’

The following object is masked from ‘package:gplots’:

reorder.factor

The following object is masked from ‘package:stats’:

nobs

The following object is masked from ‘package:utils’:

object.size

The following object is masked from ‘package:base’:

startsWith

Loading required package: mice

Attaching package: ‘mice’

The following object is masked from ‘package:stats’:

filter

The following objects are masked from ‘package:base’:

cbind, rbind

Loading required package: phangorn
Loading required package: dplyr

Attaching package: ‘dplyr’

The following objects are masked from ‘package:gdata’:

combine, first, last

The following objects are masked from ‘package:Hmisc’:

src, summarize

The following objects are masked from ‘package:stats’:

filter, lag

The following objects are masked from ‘package:base’:

intersect, setdiff, setequal, union

Error: package or namespace load failed for ‘RERconverge’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RERconverge/libs/RERconverge.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RERconverge/libs/RERconverge.so, 6): Library not loaded: /usr/local/gfortran/lib/libgfortran.3.dylib
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/RERconverge/libs/RERconverge.so
Reason: image not found

Thank you for your continued support.

@wgmao
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wgmao commented Feb 24, 2021

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.

@wgmao
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wgmao commented Feb 25, 2021 •
edited

Please follow the updated guidance https://github.com/nclark-lab/RERconverge/wiki/installand try to install from 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.

@nclark-lab
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nclark-lab commented Feb 27, 2021 via email

@wgmao
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wgmao commented Feb 28, 2021

  • 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.

@nclark-lab
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nclark-lab commented Feb 28, 2021 via email

@andypaige772
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Thank you for the update, and I apologize for the delayed response. I do not have an M1 processor. I have a 3.2 GHz 6-Core Intel Core i7.

I installed the gfortran 10.2 for Big Sur (macOS 11), for Intel processors.
I installed the binary
Screen Shot 2021-03-15 at 5 18 08 PM

I then did library(devtools), install_github("nclark-lab/RERconverge"),
Screen Shot 2021-03-15 at 5 29 22 PM
and library(RERconverge)
Screen Shot 2021-03-15 at 5 28 11 PM

Do you think there is some issue with a path for one of the programs or something simple I am missing? Thank you for your help.

Best,

@wgmao
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wgmao commented Mar 19, 2021

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.

  1. Uninstall the current RERconverge package. This should be easily done in Rstudio or you can type the following command in R
remove.packages("RERconverge")
  1. Make sure you have installed Xcode command line tools. You can install Xcode command line tools by typing xcode-select --install in the Terminal
  2. Start R or Rstudio and type the following commands.
library(devtools)
install_github("nclark-lab/RERconverge")

@andypaige772
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I removed RERconverge.
Screen Shot 2021-03-21 at 12 23 39 PM

I ensured that xcode tools were installed.
Screen Shot 2021-03-21 at 12 24 29 PM

In Rstudio I did library(devtools) and clicked Yes when the window prompted to install build tools.
Screen Shot 2021-03-21 at 12 25 08 PM
Screen Shot 2021-03-21 at 12 26 08 PM

I did install_github("nclark-lab/RERconverge") and received the following error.
Screen Shot 2021-03-21 at 12 26 15 PM

I did library("RERconverge") and received the following error.
Screen Shot 2021-03-21 at 12 27 01 PM

I then installed the binary and retried library("RERconverge") with the following error.
Screen Shot 2021-03-21 at 12 30 42 PM

Screen Shot 2021-03-21 at 12 31 59 PM
Screen Shot 2021-03-21 at 12 32 17 PM

I also tried the following with the following errors.
Screen Shot 2021-03-21 at 12 35 50 PM

Thank you for your continued support.

Best,

@wgmao
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wgmao commented Mar 24, 2021

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 gcc --version and gfortran --version to check if they are both properly installed?

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@wgmao @nclark-lab @andypaige772