Re: [R] Hacked

[Luis Puerto]

I don’t think that it’s a just a gmail issue. If some of you aren’t receiving 
those emails is probably because they get caught in your organization spam 
filter and they don’t reach you. 

Every time I write to the list I receive those messages. 

> On 18 Apr 2018, at 08:12, K. Elo <mailli...@pp.inet.fi> wrote:
> 
> Hi!
> 
> Not just an gmail issue. After my last reply I have gotten tons of
> spams from "Samantha Smith". Keep hitting my "rank as spam"-button in
> the hope that my MUA could learn :)
> 
> Best,
> Kimmo
> 
> ti, 2018-04-17 kello 19:34 +, Ding, Yuan Chun kirjoitti:
>> No, I do not use gmail, still got dirty spam email twice. 
>> 
>> -Original Message-
>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of
>> Fowler, Mark
>> Sent: Tuesday, April 17, 2018 12:32 PM
>> To: Luis Puerto; Peter Langfelder
>> Cc: R-Help ML R-Project; Neotropical bat risk assessments
>> Subject: Re: [R] Hacked
>> 
>> [Attention: This email came from an external source. Do not open
>> attachments or click on links from unknown senders or unexpected
>> emails.]
>> 
>> 
>> 
>> 
>> 
>> Just an observation. I have not seen the spam you are discussing.
>> Possibly it is specific to gmail addresses?
>> 
>> -Original Message-
>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Luis
>> Puerto
>> Sent: April 17, 2018 4:11 PM
>> To: Peter Langfelder
>> Cc: R-Help ML R-Project; Neotropical bat risk assessments
>> Subject: Re: [R] Hacked
>> 
>> Hi! 
>> 
>> This happened to me also! I just got a spam email just after posting
>> and then in following days I got obnoxious spam emails in my spam
>> filter. As the others, I think that there is some kind of bot
>> subscribed to the list, but also perhaps a spider or crawler
>> monitoring the R-Help archive and getting email addresses there.
>> Nabble is a possibility too. 
>> 
>>> 
>>> On 17 Apr 2018, at 21:50, Peter Langfelder <peter.langfelder@gmail.
>>> com> wrote:
>>> 
>>> I got some spam emails after my last post to the list, and the
>>> emails 
>>> did not seem to go through r-help. The spammers may be subscribed
>>> to 
>>> the r-help, or they get the poster emails from some of the web
>>> copies 
>>> of this list (nabble or similar).
>>> 
>>> Peter
>>> 
>>> On Tue, Apr 17, 2018 at 11:37 AM, Ulrik Stervbo <ulrik.stervbo@gmai
>>> l.com> wrote:
>>>> 
>>>> I asked the moderators about it. This is the reply
>>>> 
>>>> "Other moderators have looked into this a bit and may be able to
>>>> shed 
>>>> more light on it. This is a "new" tactic where the spammers
>>>> appear to 
>>>> reply to the r-help post. They are not, however, going through
>>>> the r-help server.
>>>> 
>>>> It also seems that this does not happen to everyone.
>>>> 
>>>> I am not sure how you can automatically block the spammers.
>>>> 
>>>> Sorry I cannot be of more help."
>>>> 
>>>> --Ulrik
>>>> 
>>>> Jeff Newmiller <jdnew...@dcn.davis.ca.us> schrieb am Di., 17.
>>>> Apr. 
>>>> 2018,
>>>> 14:59:
>>>> 
>>>>> 
>>>>> Likely a spammer has joined the mailing list and is auto-
>>>>> replying to 
>>>>> posts made to the list. Unlikely that the list itself has been 
>>>>> "hacked". Agree that it is obnoxious.
>>>>> 
>>>>> On April 17, 2018 5:01:10 AM PDT, Neotropical bat risk
>>>>> assessments < 
>>>>> neotropical.b...@gmail.com> wrote:
>>>>>> 
>>>>>> Hi all,
>>>>>> 
>>>>>> Site has been hacked?
>>>>>> Bad SPAM arriving
>>>>>> 
>>>>>> __
>>>>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more,
>>>>>> see 
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>> PLEASE do read the posting guide
>>>>>> http://www.R-project.org/posting-guide.html
>>>>>> and provide commented, minimal, self-contained, reproducible
>>>>>> code.
>>>>> --
>>>>> Sent from my pho

Re: [R] Hacked

[Luis Puerto]

Hi! 

This happened to me also! I just got a spam email just after posting and then 
in following days I got obnoxious spam emails in my spam filter. As the others, 
I think that there is some kind of bot subscribed to the list, but also perhaps 
a spider or crawler monitoring the R-Help archive and getting email addresses 
there. Nabble is a possibility too. 

> On 17 Apr 2018, at 21:50, Peter Langfelder  wrote:
> 
> I got some spam emails after my last post to the list, and the emails
> did not seem to go through r-help. The spammers may be subscribed to
> the r-help, or they get the poster emails from some of the web copies
> of this list (nabble or similar).
> 
> Peter
> 
> On Tue, Apr 17, 2018 at 11:37 AM, Ulrik Stervbo  
> wrote:
>> I asked the moderators about it. This is the reply
>> 
>> "Other moderators have looked into this a bit and may be able to shed more
>> light on it. This is a "new" tactic where the spammers appear to reply to
>> the r-help post. They are not, however, going through the r-help server.
>> 
>> It also seems that this does not happen to everyone.
>> 
>> I am not sure how you can automatically block the spammers.
>> 
>> Sorry I cannot be of more help."
>> 
>> --Ulrik
>> 
>> Jeff Newmiller  schrieb am Di., 17. Apr. 2018,
>> 14:59:
>> 
>>> Likely a spammer has joined the mailing list and is auto-replying to posts
>>> made to the list. Unlikely that the list itself has been "hacked". Agree
>>> that it is obnoxious.
>>> 
>>> On April 17, 2018 5:01:10 AM PDT, Neotropical bat risk assessments <
>>> neotropical.b...@gmail.com> wrote:
 Hi all,
 
 Site has been hacked?
 Bad SPAM arriving
 
 __
 R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
 https://stat.ethz.ch/mailman/listinfo/r-help
 PLEASE do read the posting guide
 http://www.R-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.
>>> 
>>> --
>>> Sent from my phone. Please excuse my brevity.
>>> 
>>> __
>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>> 
>> 
>>[[alternative HTML version deleted]]
>> 
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] R and Java 10 ➜ rJava not able to build

[Luis Puerto]

Thanks Peter! 

Yeah, I don’t think we users can fix this issue. Let’s wait for a fix from 
rJava team. 

Luis. 

> On 31 Mar 2018, at 17:03, peter dalgaard <pda...@gmail.com> wrote:
> 
> Don't waste too much time on this. It is due to a change introduced in Java 
> 10 at short notice. I believe the rJava maintainers are working on a 
> fix/workaround.
> 
> -pd
> 
>> On 31 Mar 2018, at 10:22 , John <j...@surewest.net> wrote:
>> 
>> On Tue, 27 Mar 2018 22:25:33 +0300
>> Luis Puerto <luiss.pue...@gmail.com> wrote:
>> 
>> I don't run a Mac so this may not help.  Did you install java 10 as
>> user or as root?  Using linux, applications installed as user will be
>> inserted into your user space under /home/.  As root the
>> application will located where any user of the system with permission
>> to run the application can access it.  I ran into a problem similar to
>> this with packages, some installed as root and some installed locally
>> in my user directory.  
>> 
>> JWDougherty
>> 
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
> 
> -- 
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: pda...@gmail.com
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] R and Java 10 ➜ rJava not able to build

[Luis Puerto]

Hi John! 

Java was installed with Homebrew Cask as a user, if my memory doesn’t fail me. 

Thanks a lot for your help! Let’s see how the problem evolves. 

> On 31 Mar 2018, at 11:22, John <j...@surewest.net> wrote:
> 
> On Tue, 27 Mar 2018 22:25:33 +0300
> Luis Puerto <luiss.pue...@gmail.com> wrote:
> 
> I don't run a Mac so this may not help.  Did you install java 10 as
> user or as root?  Using linux, applications installed as user will be
> inserted into your user space under /home/.  As root the
> application will located where any user of the system with permission
> to run the application can access it.  I ran into a problem similar to
> this with packages, some installed as root and some installed locally
> in my user directory.  
> 
> JWDougherty
> 
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] R and Java 10 ➜ rJava not able to build

[Luis Puerto]

Hi Ista! 

Thanks a lot for your support!! 

It puzzles me because it’s the first time that something like this happens to 
me. I’m aware that root and user don’t have the same environmental variables 
here. However, I don’t know why root chooses Java 9 and my user chooses Java 
10. Isn’t Java 10 ready to be used as a root? 

It seems that we are going to have to wait until rJava releases a new version 
and use Java 9 till then. I don’t have any problem with this. To be honest, I 
found out that Java jumped a version 10 because my wife was running out of 
space in her MacBook Air and checking for things to delete find she has 4 
different versions of Java 1.8, 9.0.1, 9.0.4 and 10. Then just it occurred to 
me that perhaps I could config R with Java 10 and delete all the other version. 
Also in my computer… Then was when I came across all of these. 

Again, thanks a lot for your support! 

Best Regards
Luis Puerto
http://luisspuerto.net <http://luisspuerto.net/>
> On 28 Mar 2018, at 17:04, Ista Zahn <istaz...@gmail.com 
> <mailto:istaz...@gmail.com>> wrote:
> 
> On Wed, Mar 28, 2018 at 3:56 AM, Luis Puerto <luiss.pue...@gmail.com 
> <mailto:luiss.pue...@gmail.com>> wrote:
>> Hi Jeff!!
>> 
>> I really don’t know if running R CMD javareconf with sudo has posed a 
>> problem here, now or in the past. What I know is sometimes it’s the only way 
>> to really config it, if I don’t run with sudo, in the end it asks me if I 
>> want to overwrite the configuration from root
>> 
>> override rw-r--r--  root/admin for
>> /usr/local/Cellar/r/3.4.4/lib/R/etc/Makeconf? (y/n [n]) y
>> override rw-r--r--  root/admin for
>> /usr/local/Cellar/r/3.4.4/lib/R/etc/ldpaths? (y/n [n]) y
>> 
>> So I really don’t know if this is the problem here or not.
>> 
>> I really think the problem for R is and rJava is there is no longer a javah 
>> file.
>> 
>> Unable to locate an executable at
>> "/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javah"
>> (-1)
>> 
>> Anyhow… I’m still puzzle by the fact that R CMD javareconf with sudo and 
>> without has different outcome.
> 
> Why does this puzzle you? There is no reason to expect the root user's
> environment to be the same as your user environment. You can look at
> 
> env > me.txt
> sudo env ? root.txt
> diff me.txt root.txt
> 
> to see the differences.
> 
>> 
>>> configuring Java is not on-topic here
>> 
>> I can't understand why. The problem isn’t java itself but the tool to 
>> configure R to use it with a new version.
>> 
>> Reading the released notes for Java 10:
>> 
>>> tools/javah
>>> <http://www.oracle.com/technetwork/java/javase/10-relnote-issues-4108729.html#JDK-8182758
>>>  
>>> <http://www.oracle.com/technetwork/java/javase/10-relnote-issues-4108729.html#JDK-8182758>>
>>>  JEP 313 Remove the Native-Header Generation Tool (javah)
>>> As previously announced, the native-header tool, javah, has been removed.
>>> 
>>> Native headers can now be generated by using the Java compiler, javac, with 
>>> the -h option.
>>> 
>>> See JDK-8182758 <http://bugs.java.com/view_bug.do?bug_id=JDK-8182758 
>>> <http://bugs.java.com/view_bug.do?bug_id=JDK-8182758>>
>> 
>> I don’t know if this can be fixed parsing an option in R CMD javareconf that 
>> points JAVAH to JAVAC -h
> 
> I think you're on the right track here. I tried building rJava with R
> configured to use openJDK 10 and got the same error you did. It
> appears that rJava does not currently build under openJDK 10. You did
> the right thing by opening an issue at
> https://github.com/s-u/rJava/issues/137 
> <https://github.com/s-u/rJava/issues/137> -- now you just wait to see
> what the rJava developers have to say about it. In the meantime, use
> JDK 9.
> 
> Best,
> Ista
> 
> 
>> 
>> 
>> 
>>> On 28 Mar 2018, at 04:39, Jeff Newmiller <jdnew...@dcn.davis.ca.us 
>>> <mailto:jdnew...@dcn.davis.ca.us>> wrote:
>>> 
>>> I am not a Mac user, but I do use Linux and I would recommend not running R 
>>> with sudo unless you are an admin ninja. That defensive practice would 
>>> render the answer to your question moot.
>>> 
>>> It is possible that your problem may have started with inappropriate use of 
>>> sudo in configuring java, but configuring Java is not on-topic here.
>>> --
>>> Sent from my phone. Please excuse my brevity.
>>> 
>>> On March 27, 2018 12:25:33 PM PDT, Luis Puerto <luiss.pue...@gmail.com 
>>&

Re: [R] R and Java 10 ➜ rJava not able to build

[Luis Puerto]

Hi Jeff!! 

I really don’t know if running R CMD javareconf with sudo has posed a problem 
here, now or in the past. What I know is sometimes it’s the only way to really 
config it, if I don’t run with sudo, in the end it asks me if I want to 
overwrite the configuration from root 

override rw-r--r--  root/admin for
/usr/local/Cellar/r/3.4.4/lib/R/etc/Makeconf? (y/n [n]) y
override rw-r--r--  root/admin for
/usr/local/Cellar/r/3.4.4/lib/R/etc/ldpaths? (y/n [n]) y

So I really don’t know if this is the problem here or not. 

I really think the problem for R is and rJava is there is no longer a javah 
file. 

Unable to locate an executable at
"/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javah"
(-1)

Anyhow… I’m still puzzle by the fact that R CMD javareconf with sudo and 
without has different outcome. 

> configuring Java is not on-topic here

I can't understand why. The problem isn’t java itself but the tool to configure 
R to use it with a new version. 

Reading the released notes for Java 10: 

> tools/javah
>  
> <http://www.oracle.com/technetwork/java/javase/10-relnote-issues-4108729.html#JDK-8182758>
>  JEP 313 Remove the Native-Header Generation Tool (javah) 
> As previously announced, the native-header tool, javah, has been removed.
> 
> Native headers can now be generated by using the Java compiler, javac, with 
> the -h option.
> 
> See JDK-8182758 <http://bugs.java.com/view_bug.do?bug_id=JDK-8182758>

I don’t know if this can be fixed parsing an option in R CMD javareconf that 
points JAVAH to JAVAC -h 



> On 28 Mar 2018, at 04:39, Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote:
> 
> I am not a Mac user, but I do use Linux and I would recommend not running R 
> with sudo unless you are an admin ninja. That defensive practice would render 
> the answer to your question moot.
> 
> It is possible that your problem may have started with inappropriate use of 
> sudo in configuring java, but configuring Java is not on-topic here.
> -- 
> Sent from my phone. Please excuse my brevity.
> 
> On March 27, 2018 12:25:33 PM PDT, Luis Puerto <luiss.pue...@gmail.com 
> <mailto:luiss.pue...@gmail.com>> wrote:
>> Hi! 
>> 
>> I’m on macOS 10.13.3 and just installed the new Java 10 using Homebrew
>> Cask. I also have installed R with Homebrew. Everything seems to work
>> fine, however I just get different outputs if I run sudo R CMD
>> javareconf or R CMD javareconf. With sudo I get pointed to Java 9 and
>> without sudo I get pointed to Java 10. I really don’t know why. 
>> 
>> Without sudo:
>> 
>> $ R CMD javareconf 
>> 
>> Java interpreter :
>> /Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/java
>> Java version : 10
>> Java home path   :
>> /Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home
>> Java compiler:
>> /Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javac
>> Java headers gen.: /usr/bin/javah
>> Java archive tool:
>> /Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/jar
>> Non-system Java on macOS
>> 
>> trying to compile and link a JNI program
>> detected JNI cpp flags: -I$(JAVA_HOME)/include
>> -I$(JAVA_HOME)/include/darwin
>> detected JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
>> /usr/local/opt/llvm/bin/clang 
>> -I/usr/local/Cellar/r/3.4.4/lib/R/include -DNDEBUG
>> -I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include
>> -I/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/include/darwin
>> -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include   -fPIC 
>> -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c conftest.c -o
>> conftest.o
>> /usr/local/opt/llvm/bin/clang++ -dynamiclib
>> -Wl,-headerpad_max_install_names -undefined dynamic_lookup
>> -single_module -multiply_defined suppress -L/usr/local/opt/gettext/lib
>> -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib
>> -L/usr/local/Cellar/r/3.4.4/lib/R/lib -L/usr/local/opt/gettext/lib
>> -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o
>> conftest.so conftest.o
>> -L/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/lib/server
>> -ljvm -L/usr/local/Cellar/r/3.4.4/lib/R/lib -lR -lintl -Wl,-framework
>> -Wl,CoreFoundation
>> 
>> 
>> JAVA_HOME:
>> /Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home
>> Java library path: $(JAVA_HOME)/lib/server
>> JNI cpp flags: -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/darwin
>> JNI linker flags : -L$(JAVA_HOME)/lib/server -ljvm
>> Updating Java configuration in 

[R] R and Java 10 ➜ rJava not able to build

[Luis Puerto]

 files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
4 warnings
/usr/bin/javah -d . -classpath . org.rosuda.JRI.Rengine
Unable to locate an executable at 
"/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javah" (-1)
make[2]: *** [org_rosuda_JRI_Rengine.h] Error 2
make[1]: *** [src/JRI.jar] Error 2
make: *** [jri] Error 2
ERROR: compilation failed for package ‘rJava’
* removing ‘/Users/lpuerto/Library/R/3.x/library/rJava’
* restoring previous ‘/Users/lpuerto/Library/R/3.x/library/rJava’

The downloaded source packages are in

‘/private/var/folders/wf/41gjf2mx7m7fmvfd8dr22_5hgn/T/RtmpT2kJMY/downloaded_packages’
Warning message:
In install.packages("rJava", repos = "cloud.r-project.org") :
  installation of package ‘rJava’ had non-zero exit status
I've checked and there isn't a javah on 
/Library/Java/JavaVirtualMachines/jdk-10.jdk/Contents/Home/bin/javah as in Java 
9. Which make me think that either R CMD javareconf isn’t working properly with 
Java 10 or rJava is not yet compatible with Java 10. 

Does anyone know what is going on? 

Thanks! 

PS/ I’ve opened an issue <https://github.com/s-u/rJava/issues/137> in rJava’s 
github and a question in stackoverflow 
<https://stackoverflow.com/questions/49519007/sudo-r-cmd-javareconf-and-r-cmd-javareconf-produce-different-output-with-java-10>.
 


Best Regards
Luis Puerto
http://luisspuerto.net


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[R] Pin package/s

[Luis Puerto]

Hi! 

I don’t know if you know package manager for macOS Homebrew. With Homebrew 
there is a way to stop update certain packages: 

brew pin 

Does anyone know a way to do a similar thing with R packages? 

In the same way, it would be great to be able to receive a notification –an 
email– when a new version of a package reach CRAN or any other repository. 

I would like to have something like this because the Data Table package has a 
certain makevars necessities when it’s built in a Homebrew R install. It isn’t 
really problematic since it the package hasn’t built correctly when you load it 
on R it will display a message. However, I’m thinking that perhaps something 
like this could be useful also for other packages. 

Thanks! 


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