[Rd] failure to find lapply (PR#9999)

From: <chris.knight_at_manchester.ac.uk>
Date: Thu, 11 Oct 2007 11:11:31 +0200 (CEST)


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 
www.dbkgroup.org/MCISB/people/knight/                   `  . ,,><(((>

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Received on Thu 11 Oct 2007 - 20:07:04 GMT

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