[R-meta] error installing devel version of metafor

Gram, Gil (IITA) G@Gr@m @ending from cgi@r@org
Thu Nov 15 12:18:02 CET 2018

Hi Wolfgang,

It indeed seems to be not related to metafor, as it also doesn’t work for another package I tried. Have been trying to figure out the problem, but couldn’t find much (specific) help. I downloaded therefore the dev package metafor-master manually from https://github.com/wviechtb/metafor, and installed/loaded it as shown below. Two questions:
(1) I could not run cooks.distance.rma.mv() because of a new error (see below)
(2) profile.rma.mv() had a similar problem as cd with the 2.0-0 version, i.e. it was running for days without showing signs of progress. You think this should also go faster with the dev version 2.1-0?


> packageVersion("metafor")
[1] '2.1.0'

> class(modRE_6)
[1] "rma.mv" “rma”
> summary(modRE_6)
Multivariate Meta-Analysis Model (k = 5130; method: REML)
coefficients 1:30

> cooks.distance.rma.mv(modRE_6, progbar=T)
Error in seq_len(x$k.all) :
  argument must be coercible to non-negative integer
In addition: Warning message:
In seq_len(x$k.all) : first element used of 'length.out' argument

Your help is appreciated.

Gil Gram
PhD researcher  |  Natural resource management/CCAFS
International Institute of Tropical Agriculture (IITA)
East African Hub/Kampala/Country office
Address: IITA-Uganda Plot 15B, Naguru East Road. P.O Box 7878, Kampala
Mobile: +256 755 315236  |  Belgium Mobile: +32 484 981200
Skype: gil.gram

On 14 Nov 2018, at 18:53, Viechtbauer, Wolfgang (SP) <wolfgang.viechtbauer using maastrichtuniversity.nl<mailto:wolfgang.viechtbauer using maastrichtuniversity.nl>> wrote:

Dear Gil,

This doesn't look like it is related to metafor per se. Can you install other packages via install_github()? Have you tried updating devtools (in case it is not the newest version)?


-----Original Message-----
From: R-sig-meta-analysis [mailto:r-sig-meta-analysis-bounces using r-project.org] On Behalf Of Gram, Gil (IITA)
Sent: Tuesday, 13 November, 2018 8:43
To: r-sig-meta-analysis using r-project.org<mailto:r-sig-meta-analysis using r-project.org>
Subject: [R-meta] error installing devel version of metafor

Dear community and Wolfgang,

I’m trying to compute the cook’s distances for my pretty complex rma.mv model (for context, running the model with sparse=TRUE still takes about 12 hours). However, after a few days still at 0% I assume it’s not going well. I read that cooks.distance.rma.mv is indeed slow on complex models (https://stat.ethz.ch/pipermail/r-sig-meta-analysis/2017-August/000122.html) and Wolfgang suggested to install the devel version of metafor with install.packages("devtools") and devtools::install_github("wviechtb/metafor”). Unfortunately I get the following error: “> devtools::install_github("wviechtb/metafor")
Downloading GitHub repo wviechtb/metafor using master tar: Failed to set default locale tar: Failed to set default locale During startup - Warning messages: 1: Setting LC_CTYPE failed, using "C" 2: Setting LC_TIME failed, using "C" 3: Setting LC_MESSAGES failed, using "C" 4: Setting LC_MONETARY failed, using "C" v checking for file '/private/var/folders/wz/t5wd352s5wl7tz7crj5r3ddr0000gn/T/Rtmp8x3jdd/remotesfda76b9f309/wviechtb-metafor-e153805/DESCRIPTION' ... - preparing 'metafor': v checking DESCRIPTION meta-information ... - checking for LF line-endings in source and make files and shell scripts - checking for empty or unneeded directories - looking to see if a 'data/datalist' file should be added - building 'metafor_2.1-0.tar.gz'

Error: (converted from warning) Setting LC_CTYPE failed, using "C"
Execution halted Error in i.p(...) : (converted from warning) installation of package '/var/folders/wz/t5wd352s5wl7tz7crj5r3ddr0000gn/T//Rtmp8x3jdd/filefda18e204cb/metafor_2.1-0.tar.gz' had non-zero exit status”

Tried to look for other ways of installing it, but in vain. Hope someone can help with this? Not sure what other information I should provide...


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