chris.knight at manchester.ac.uk
2007-Oct-11 09:11 UTC
[Rd] failure to find lapply (PR#9999)
I have been unable to reproduce this problem but the warning I got told
me to send a bug report, so here it is.
After a fairly lengthy session, using the ape and ade4 packages,
conducted via a terminal in kate under kubuntu 6.06 linux , I found
errors claiming not to find lapply- see first section below.
...
> if(nas>0){
+ tree<-drop.tip(tree,tip=which(is.na(scorei)))
+ scorei<-scorei[which(!is.na(scorei))]
+ }
Error in paste("as.", value, sep = "") : could not find
function "lapply"
> tree2<-newick2phylog(write.tree(tree, multi.line=FALSE))
Error in paste("%.", digits, "g", sep = "") :
could not find function "lapply"
> n<-length(tree$tip.label)-1
> e<-rep(NA,n)
> k<-1/(1:n)
> for(j in 1:n){
+ Error in sapply(c("(", ")"), function(s) gregexpr(s,
substr(line, 1,
cursor), :
could not find function "lapply"
> e[j]<-sum(k[j:n])
Error: object "j" not found
> Error in sapply(c("(", ")"), function(s) gregexpr(s,
substr(line, 1,
cursor), :
could not find function "lapply"
> }
...
This continued in a similar vein as I had pasted in quite a few lines
until the warning suggesting a bug report (below).
As can be seen below, this error prevented directly calling either
bug.report() or sessionInfo(), however the R.version output was possible
and the output from bug.report() and sessionInfo() from another session
started just after on the same machine are given below:
...
> tree<-drop.tip(tree,tip=which(is.na(scorei)))
Error in paste("as.", value, sep = "") : could not find
function "lapply"
> Error in sapply(c("(", ")"), function(s) gregexpr(s,
substr(line, 1,
cursor), :
could not find function "lapply"
> scorei<-scorei[which(!is.na(scorei))]
Warning message:
An unusual circumstance has arisen in the nesting of readline input.
Please report using bug.report()
> bug.report()
Error in paste(names(R.version), R.version, sep = " = ", collapse =
"\\n
") :
could not find function "lapply"
> lapply
[[1]]
Error in paste("Error in", dcall, ": ") :
could not find function "lapply"
>
> sessionInfo()
Error in sapply(package, function(x) x == "package:base" ||
!is.null(attr(as.environment(x), :
could not find function "lapply"
> R.version
_
platform i486-pc-linux-gnu
arch i486
os linux-gnu
system i486, linux-gnu
status
major 2
minor 6.0
year 2007
month 10
day 03
svn rev 43063
language R
version.string R version 2.6.0 (2007-10-03)
...
sessionInfo() from another, similar session:
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ade4_1.4-4 lattice_0.16-5 nlme_3.1-85 gee_4.13-13 ape_2.0-1
loaded via a namespace (and not attached):
[1] grid_2.6.0 rcompgen_0.1-15
From bug.report() in another session
--please do not edit the information below--
Version:
platform = i486-pc-linux-gnu
arch = i486
os = linux-gnu
system = i486, linux-gnu
status major = 2
minor = 6.0
year = 2007
month = 10
day = 03
svn rev = 43063
language = R
version.string = R version 2.6.0 (2007-10-03)
Locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
Search Path:
.GlobalEnv, package:ade4, package:lattice, package:nlme, package:gee,
package:ape, package:stats, package:graphics, package:grDevices,
package:utils, package:datasets, package:methods, Autoloads, package:base
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"R.bug.report" 27L, 783C 4,0-1 All
--
------------------------------------------------------------------------
Dr Christopher Knight Manchester Interdisciplinary Biocentre
room 2.001 The University of Manchester
Tel: +44 (0)161 3065138 131 Princess Street
Fax: +44 (0)161 3064556 Manchester M1 7DN
chris.knight at manchester.ac.uk UK
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