Why does rownames(installed.packages()) have a names attribute?

Question

I have the following function for personal use. It takes in an author's name to see if I have any of their packages on my machine.

authoredPackages <- function (author) 
{
    s <- sapply(rownames(installed.packages()), 
        packageDescription, fields = "Author")
    names(grep(author, s, value = TRUE))
}

Here's the problem. Upon opening a new R session and assigning the function, the first call to the function always returns a character vector of empty strings the correct length of the vector it's supposed to return. To show this, open a new R session, assign the function, and run it with your favorite package author's surname. It should first return an empty character vector ...

authoredPackages("Temple Lang")
# [1] "" "" "" ""

... and then do it again and it returns the correct result ...

authoredPackages("Temple Lang")
# [1] "jsonlite" "RCurl"    "RJSONIO"  "XML"

It always only happens on the first call in a new R session. Why does this happen, and how can I fix it so the function always works on the first try?

My R --vanilla session info:

R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

Update: Upon opening R, is seems rownames(installed.packages()) has a names attribute because of the lme4 package. Not sure why, and it's the only name. It's also very strange how it disappears on the second call.

rownames(installed.packages())[228]
#   ret0 
# "lme4"

Starting with R --vanilla? `sessionInfo()`? for me `authoredPackages()` works as expected for R version 3.1.2 Patched (2014-10-31 r66919) / Platform: x86_64-unknown-linux-gnu (64-bit) and R Under development (unstable) (2014-11-23 r67046) / Platform: x86_64-unknown-linux-gnu (64-bit) — Martin Morgan, Nov 25 '14 at 00:27
seems like `ret0` is mentioned in the `installed.packages` source, when noCache=FALSE toward the end of the function; maybe adding `noCache=TRUE` as an argument is a work-around? — Martin Morgan, Nov 25 '14 at 01:45
@MartinMorgan: Nice guess, but adding `noCache=TRUE` still yields the same odd results for me. — Joshua Ulrich, Nov 25 '14 at 13:37

score 7 · Accepted Answer · edited May 23 '17 at 11:46

Odd, but seems like rownames(installed.packages()) has a names attribute the first time you call it.

> str(rownames(installed.packages()))
 Named chr [1:125] "bdsmatrix" "bitops" "blotter" "brew" "car" "changepoint" "chron" "colorout" ...
 - attr(*, "names")= chr [1:125] "" "" "" "" ...
> str(rownames(installed.packages()))
 chr [1:125] "bdsmatrix" "bitops" "blotter" "brew" "car" "changepoint" "chron" "colorout" "colorspace" ...

Sorry, that left it to you to answer the question. Just make sure there are no names. This is a problem for you because you're relying on sapply's default of USE.NAMES=TRUE, but that only adds names if they're not already present. And they're present for some really weird reason.

authoredPackages <- function (author) 
{
    r <- setNames(rownames(installed.packages()), NULL)
    s <- sapply(r, function(x) packageDescription(x)$Author)
    names(grep(author, s, value = TRUE))
}

Here's my sessionInfo (from starting with R --vanilla):

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] tools_3.1.1

I just upgraded to R-3.1.2 and tried again. I still get the same odd results, and I get them consistently if I use @MartinMorgan's suggestion to use noCache=TRUE.

> str(rownames(installed.packages(noCache=TRUE)))
 Named chr [1:125] "bdsmatrix" "bitops" "blotter" "brew" "car" "changepoint" "chron" "colorout" ...
 - attr(*, "names")= chr [1:125] "" "" "" "" ...
> str(rownames(installed.packages(noCache=TRUE)))
 Named chr [1:125] "bdsmatrix" "bitops" "blotter" "brew" "car" "changepoint" "chron" "colorout" ...
 - attr(*, "names")= chr [1:125] "" "" "" "" ...
> str(rownames(installed.packages(noCache=TRUE)))
 Named chr [1:125] "bdsmatrix" "bitops" "blotter" "brew" "car" "changepoint" "chron" "colorout" ...
 - attr(*, "names")= chr [1:125] "" "" "" "" ...
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] setwidth_1.0-3 colorout_1.0-1

loaded via a namespace (and not attached):
[1] tools_3.1.2

Why does rownames(installed.packages()) have a names attribute?

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