R help - Sep 2019 - Bug (?): file.copy() erases 'from' file if the "to" file already exists and is a symlinked file

If file.copy() is used to replace a symlinked file, it erases the 
original file and does not copy the file. The original file is lost.

 > version
 ???????????????????????????? _
platform???????????? x86_64-apple-darwin15.6.0
arch???????????????????? x86_64
os???????????????????????? darwin15.6.0
system???????????????? x86_64, darwin15.6.0
status???????????????? Patched
major?????????????????? 3
minor?????????????????? 6.1
year???????????????????? 2019
month?????????????????? 09
day?????????????????????? 06
svn rev?????????????? 77160
language???????????? R
version.string R version 3.6.1 Patched (2019-09-06 r77160)
nickname???????????? Action of the Toes

#########################

Here is a reproducible example:

A <- 10
save(A, file="A.Rdata")
file.symlink(from="A.Rdata", to="B.Rdata")
rm(A)

load(file="B.Rdata")
print(A)?????????????????????? # Perfect

system("ls -l")
## -rw-r--r--?? 1 marcgirondot?? staff?????????? 70 13 sep 11:44 A.Rdata
## lrwxr-xr-x?? 1 marcgirondot?? staff???????????? 7 13 sep 11:44 B.Rdata ->
A.Rdata

file.copy(from="A.Rdata", to="B.Rdata", overwrite = TRUE)

system("ls -l")
## -rw-r--r--?? 1 marcgirondot?? staff???????????? 0 13 sep 11:44 A.Rdata
## lrwxr-xr-x?? 1 marcgirondot?? staff???????????? 7 13 sep 11:44 B.Rdata ->
A.Rdata

###############

A.Rdata becomes empty: 0B
The content of A.Rdata is lost

################
In terminal the problem does not occur
################

marcgirondot$ ls
A.Rdata
marcgirondot$ ln -s A.Rdata B.Rdata
marcgirondot$ ls -l
-rw-r--r--?? 1 marcgirondot?? staff?????????? 70 13 sep 11:38 A.Rdata
lrwxr-xr-x?? 1 marcgirondot?? staff???????????? 7 13 sep 11:38 B.Rdata ->
A.Rdata
marcgirondot$ cp A.Rdata B.Rdata
cp: B.Rdata and A.Rdata are identical (not copied).

However, notice that cat doesn't protect you in the same way:

Peters-iMac:tst pd$ echo stuff > A
Peters-iMac:tst pd$ ln -s A B
Peters-iMac:tst pd$ ls -l
total 8
-rw-r--r--  1 pd  staff  6 Sep 13 15:20 A
lrwxr-xr-x  1 pd  staff  1 Sep 13 15:20 B -> A
Peters-iMac:tst pd$ cp A B
cp: B and A are identical (not copied).
Peters-iMac:tst pd$ ls -l
total 8
-rw-r--r--  1 pd  staff  6 Sep 13 15:20 A
lrwxr-xr-x  1 pd  staff  1 Sep 13 15:20 B -> A
Peters-iMac:tst pd$ cat A > B
Peters-iMac:tst pd$ ls -l
total 0
-rw-r--r--  1 pd  staff  0 Sep 13 15:20 A
lrwxr-xr-x  1 pd  staff  1 Sep 13 15:20 B -> A

(& I suspect that cp did likewise in early Unices). Bug or not, it would be
good if we could detect when "from" and "to" refer to the
same file, but I'm not sure how to do that.

-pd
> On 13 Sep 2019, at 11:56 , Marc Girondot via R-help <r-help at
r-project.org> wrote:
> 
> If file.copy() is used to replace a symlinked file, it erases the original
file and does not copy the file. The original file is lost.
> 
> > version
> ???????????????????????????? _
> platform???????????? x86_64-apple-darwin15.6.0
> arch???????????????????? x86_64
> os???????????????????????? darwin15.6.0
> system???????????????? x86_64, darwin15.6.0
> status???????????????? Patched
> major?????????????????? 3
> minor?????????????????? 6.1
> year???????????????????? 2019
> month?????????????????? 09
> day?????????????????????? 06
> svn rev?????????????? 77160
> language???????????? R
> version.string R version 3.6.1 Patched (2019-09-06 r77160)
> nickname???????????? Action of the Toes
> 
> #########################
> 
> Here is a reproducible example:
> 
> A <- 10
> save(A, file="A.Rdata")
> file.symlink(from="A.Rdata", to="B.Rdata")
> rm(A)
> 
> load(file="B.Rdata")
> print(A)?????????????????????? # Perfect
> 
> system("ls -l")
> ## -rw-r--r--?? 1 marcgirondot?? staff?????????? 70 13 sep 11:44 A.Rdata
> ## lrwxr-xr-x?? 1 marcgirondot?? staff???????????? 7 13 sep 11:44 B.Rdata
-> A.Rdata
> 
> file.copy(from="A.Rdata", to="B.Rdata", overwrite =
TRUE)
> 
> system("ls -l")
> ## -rw-r--r--?? 1 marcgirondot?? staff???????????? 0 13 sep 11:44 A.Rdata
> ## lrwxr-xr-x?? 1 marcgirondot?? staff???????????? 7 13 sep 11:44 B.Rdata
-> A.Rdata
> 
> ###############
> 
> A.Rdata becomes empty: 0B
> The content of A.Rdata is lost
> 
> ################
> In terminal the problem does not occur
> ################
> 
> marcgirondot$ ls
> A.Rdata
> marcgirondot$ ln -s A.Rdata B.Rdata
> marcgirondot$ ls -l
> -rw-r--r--?? 1 marcgirondot?? staff?????????? 70 13 sep 11:38 A.Rdata
> lrwxr-xr-x?? 1 marcgirondot?? staff???????????? 7 13 sep 11:38 B.Rdata
-> A.Rdata
> marcgirondot$ cp A.Rdata B.Rdata
> cp: B.Rdata and A.Rdata are identical (not copied).
> 
> ______________________________________________
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com