That Rscript stalls sounds like a bug, but not sure it's R or the
terminal that needs to be fixed:
Rscript -e "$long_expression"
WARNING: '-e
{x~+~<-~+~c(-1.31171,~+~-0.686165,~+~1.62771,~+~0.320195,~+~-0.322011,~+~1.66518,~+~-0.271971,~+~-0.665367,~+~0.516482,~+~-0.716343,~+~-0.317471,~+~0.068046,~+~-0.100371,~+~-1.15907,~+~0.263329,~+~-0.936049,~+~-0.852444,~+~0.358817,~+~-0.233959,~+~0.209891,~+~-0.831575,~+~-0.952987,~+~-0.0420206,~+~-1.78527,~+~-0.280584,~+~-0.62353,~+~1.42597,~+~0.127994,~+~0.0751232,~+~0.896835,~+~-0.319488,~+~0.897876,~+~0.18457,~+~0.779571,~+~-0.0543194,~+~0.226722,~+~-0.769983,~+~-0.723463,~+~0.144386,~+~-0.468544,~+~-0.349417,~+~0.336786,~+~0.749212,~+~-1.62397,~+~0.683075,~+~-0.746449,~+~0.300921,~+~-0.365468,~+~0.548271,~+~1.13169,~+~-1.34042,~+~-0.0740572,~+~1.34986,~+~0.531771,~+~-0.147157,~+~0.824894,~+~-1.05816,~+~1.58867,~+~-0.885764,~+~1.11912,~+~0.361512,~+~1.77985,~+~0.585099,~+~-1.205,~+~2.44134,~+~-0.331372,~+~-0.346322,~+~0.0535267,~+~-1.75089,~+~0.0773243,~+~-1.07846,~+~-1.29632,~+~1.0622,~+~1.34867,~+~0.199777,~+~0.197516,~+~0.574185,~+~1.06555,~+~-0.885166,~+~-0.788576,~+~-1.46061,~+~-1.5402
^C^C
^C
^C^C^C^C^C^C
^\Quit (core dumped)
On my default Ubuntu 16.04 terminal, R 3.3.3 hangs and does not
respond to user interrupts (SIGINT), but it does respond to Ctrl-\
(SIGKILL).
A workaround is to pass the expression via standard input to R, e.g.
$ echo "$long_expression" | R --no-save
/Henrik
On Fri, Apr 21, 2017 at 11:07 AM, Ben Tupper <btup...@bigelow.org> wrote:
> Hi,
>
> I suspect you are over the 10kb limit for the expression. See
>
> https://cran.r-project.org/doc/manuals/r-release/R-intro.html#Invoking-R-from-the-command-line
>
> Cheers,
> Ben
>
>> On Apr 21, 2017, at 3:44 AM, Ben Haller <bhal...@mac.com> wrote:
>>
>> Hi! I’m attempting to use Rscript to do some automated plotting. It is
>> working well, except that I seem to be running into a maximum line length
>> issue, and I’m wondering if it is a bug on your end. Here’s an example of
>> the command I’m trying to run:
>>
>> /usr/local/bin/Rscript -e '{x <- c(-1.31171, -0.686165, 1.62771, 0.320195,
>> -0.322011, 1.66518, -0.271971, -0.665367, 0.516482, -0.716343, -0.317471,
>> 0.068046, -0.100371, -1.15907, 0.263329, -0.936049, -0.852444, 0.358817,
>> -0.233959, 0.209891, -0.831575, -0.952987, -0.0420206, -1.78527, -0.280584,
>> -0.62353, 1.42597, 0.127994, 0.0751232, 0.896835, -0.319488, 0.897876,
>> 0.18457, 0.779571, -0.0543194, 0.226722, -0.769983, -0.723463, 0.144386,
>> -0.468544, -0.349417, 0.336786, 0.749212, -1.62397, 0.683075, -0.746449,
>> 0.300921, -0.365468, 0.548271, 1.13169, -1.34042, -0.0740572, 1.34986,
>> 0.531771, -0.147157, 0.824894, -1.05816, 1.58867, -0.885764, 1.11912,
>> 0.361512, 1.77985, 0.585099, -1.205, 2.44134, -0.331372, -0.346322,
>> 0.0535267, -1.75089, 0.0773243, -1.07846, -1.29632, 1.0622, 1.34867,
>> 0.199777, 0.197516, 0.574185, 1.06555, -0.885166, -0.788576, -1.46061,
>> -1.54026, 0.690576, -0.88821, 0.343747, -0.100751, -0.865596, -0.128504,
>> 0.222334, -1.18932, -0.555258, -0.557368, 0.219272, 0.298858, 0.848022,
>> 0.142608, 1.10082, -0.348039, 0.0566489, 0.662136, 0.50451, -0.909399,
>> 1.02446, 1.40592, -0.114786, -1.10718, 2.02549, 0.0818607, -1.037, 1.18961,
>> -0.204, 2.83165, -0.959653, -0.393082, -0.463351, 0.914054, 1.14472,
>> -1.32927, 1.25416, 0.372267, 0.410832, 1.04187, 1.22288, 1.27131, 0.0949385,
>> 0.194053, -0.226184, -0.502155, -1.36834, -0.000591861, -0.565903, 1.14099,
>> 1.67811, 0.331709, -0.756879, 0.889596, 0.718098, 0.740242, -0.861818,
>> 0.0332746, 1.01745, 0.584536, -1.14245, -0.444485, -1.34237, 0.660603,
>> 1.16048, -0.898828, 0.965746, -1.16953, -2.33417, 0.591078, -0.364892,
>> 0.0719267, -1.21676, 1.12646, 1.37534, 0.0712832, 1.22889, -0.0110024,
>> 0.248213, -1.12013, -0.525197, -0.352156, -0.317182, -0.89552, 1.53422,
>> -1.36777, 1.52099, 1.18789, -3.15251, 1.24008, -0.564289, -0.515629,
>> -0.0920464, 2.94027, 0.895481, -0.157643, -0.347874, -0.290823, -0.771436,
>> 1.29285, 0.216689, -1.86856, 2.24075, 0.888635, 0.430417, -0.585856,
>> 1.13119, -0.243977, 0.544491, 0.921995, 0.815365, 1.2584, -1.29347,
>> 0.0574579, 0.990557, -1.58657, -0.264373, 0.865893, 0.599298, -0.417531,
>> 0.132897, 1.88597, 1.33112, -0.880904, 0.0762161, 0.0567852, 0.593295,
>> -0.632135, 0.885625, 0.365863, -0.17885, 0.420185, -0.508275, 0.974357,
>> 0.628085, 0.710578, 1.72447, 1.38488, 1.01301, 1.30015, 0.260501, 0.808981,
>> 0.440228, 0.416344, -1.66273, -0.397224, -0.512086, -0.175854, -0.663143,
>> 0.369712, -1.01654, 0.660465, 0.124851, -1.51101, -0.95725, 2.09893,
>> 1.26819, 1.08086, 0.493204, 0.79073, 1.49191, 0.563689, 0.414473, 2.27361,
>> 0.871923, 0.193703, -0.185039, -0.312859, -1.42267, -2.11561, 0.311996,
>> -0.0906527, 1.19139, 1.57502, 1.10587, 0.416333, 2.35374, -1.0531,
>> 0.0450512, 0.979958, 0.398269, 0.0897618, -0.855305, -1.59337, -0.084904,
>> 0.245872, 1.27115, 1.3512, -0.166962, 1.01098, -1.19854, -2.05932, -0.98,
>> 0.704973, 0.694688, 1.20408, -1.12553, 0.770056, 1.01602, 0.295223,
>> -1.18801, 1.51707, 1.1418, -0.148787, 1.28886, 1.23981, 1.67984, 0.0185941,
>> -0.877581, 0.495042, -0.368668, 1.59972, -2.20849, -1.36852, -0.972566,
>> -1.01848, -0.366674, -2.60273, -0.540706, -0.475797, 0.227651, -1.11476,
>> 1.73452, -0.212185, 3.04994, -0.251225, -0.0443482, -0.489125, 0.557936,
>> -0.246389, -0.954287, 0.388668, 0.759049, -0.501683, -1.98722, 0.158712,
>> -0.897082, -1.17644, 0.192465, -1.49901, -0.289129, -0.0460198, -0.520331,
>> 0.432488, -0.471775, 1.21482, 0.998091, -0.794933, -0.36989, 0.937091,
>> 1.27297, 1.06108, -0.784307, 0.70919, -0.309221, -0.516031, 0.479702,
>> -0.669637, 1.60288, 0.657474, -0.666286, -1.01816, -0.452818, -0.283749,
>> 1.05511, -1.2002, 0.112269, -1.37403, 1.00512, 0.664936, 0.600516, -1.08099,
>> -0.705522, 0.103051, 0.0461179, 1.74404, 0.727475, 2.41175, 1.20414,
>> 1.71095, 0.0957544, 0.610755, 0.545194, -0.936381, 0.190467, 0.485791,
>> 0.0855697, 0.142676, 0.721754, -1.84506, 2.1227, -1.1271, -1.11228, -1.2807,
>> 0.13385, 0.228727, -0.34391, 1.09837, -0.37053, 0.832574, 0.673463,
>> 0.717732, -0.307687, 1.12486, 0.159803, -1.51251, 1.403, 2.0215, 0.010914,
>> -0.543749, 0.137119, 0.200364, -0.104029, -0.930966, -1.56781, -0.526978,
>> -0.537582, 1.11872, -0.99061, -0.501421, 1.21982, 0.813201, -0.539109,
>> 0.433523, -0.0615188, 2.04298, 0.697692, 1.34515, 1.7298, 0.515137, 2.08119,
>> 0.550985, 1.49876, 1.31187, 0.920405, 0.597678, 0.884353, -0.732892,
>> -0.143545, -0.236836, -0.330872, 1.55577, -1.74473, -0.493322, 1.46375,
>> 1.14347, 1.76164, 1.73099, -0.234701, -0.0546848, 0.346991, -0.393301,
>> 1.34267, -1.58519, -0.381789, 0.622675, 1.34655, 2.84895, -0.371, -0.519666,
>> -1.64944, 0.573592, 1.06484, -0.0239894, -0.604563, 0.0680641, -0.881325,
>> 1.07265, 0.182585, 0.373288, 2.20228, -0.763593, -0.25659, 1.9397,
>> -0.166943, -0.672522, -1.35983, 0.227406, 0.49471, -1.23535, -0.479552,
>> 1.97798, 0.418181, 1.23454, -0.0767748, 0.828642, -0.0348468, -0.264499,
>> 0.76699, -0.910363, -2.11408, -0.209169, 0.902191, -2.27096, 0.098513,
>> -0.380699, -0.231276, -0.0296834, 0.834972, -0.658283, 0.616493, 0.198916,
>> -1.89783, -1.30219, 0.51036, 0.195825, -1.68961, -1.27838, 0.879616,
>> 0.566719, 1.21876, 0.270402, -1.38261, 0.365878, 1.54191, 1.25104, 1.23067,
>> 1.87261);y <- c(0.986442, 2.65684, -1.79726, 1.79999, -2.43971, -1.68358,
>> -1.84081, -2.27973, 2.96046, 2.61837, 1.48756, 1.63497, 1.46876, 2.09348,
>> -0.925101, 3.6792, -2.03618, 1.33232, -0.0652269, 0.809911, -2.82019,
>> -1.87691, 1.1284, 0.249619, -2.94777, 3.00423, -2.79901, -0.110801, -3.546,
>> 1.67156, -3.10723, -3.24205, 3.16911, -3.24227, -1.29801, 0.271933,
>> -2.83573, -0.79973, -2.34429, -0.905163, -0.197905, -3.05664, -0.694481,
>> 1.89301, -2.70264, 2.94361, -2.32469, 1.9576, 1.73556, -3.29777, -1.54311,
>> -2.03172, -0.871756, 0.77581, 3.7692, 1.54446, 3.92129, 0.160296, -3.45486,
>> -1.56317, -2.72913, 0.695854, 3.15786, 1.1006, 3.25649, -1.57206, -3.15353,
>> 0.242301, -1.95855, -0.256919, 3.04782, -0.505045, -2.35542, 2.11649,
>> -1.73363, 2.65149, 3.66302, 0.457907, -2.2759, -2.36105, -2.49263, -2.9784,
>> -3.53525, -0.699404, 3.17647, -1.52424, 2.72699, 3.82774, 0.100029, 3.42107,
>> 1.74672, 3.1279, -0.793162, -0.025109, 1.07262, 2.4517, -2.00605, -3.6625,
>> -2.57031, -2.43599, 2.56309, -1.31707, -2.10777, -3.75394, 0.954311,
>> 0.496025, 3.82545, -3.74259, -1.96145, 0.366455, 3.97474, 3.26111, -3.69904,
>> 2.07392, 0.591191, -3.34162, -0.926126, 1.03966, -2.68754, -2.69653,
>> 0.651845, 2.82333, 2.25596, 3.26545, -2.57379, 2.69137, -3.08119, 2.99114,
>> -3.86005, -1.30995, 1.80096, 1.39404, -2.6482, -2.12922, -3.28834, -1.06563,
>> -1.6683, -2.023, 1.60516, -1.67431, 1.38595, 0.287423, 2.56888, -2.99169,
>> 0.549401, 2.31817, -2.48251, 2.20152, 1.0531, -3.60478, 0.327999, 0.475523,
>> -0.454324, -2.63147, -1.61249, -1.65507, 1.13203, 0.218, 2.87289, -0.279036,
>> -0.316795, 3.22757, -2.25, -1.10923, 0.0949814, -2.60818, -0.181803,
>> 3.65484, 2.86193, 0.940815, 3.5461, 1.23983, 2.01177, -0.428626, 3.5539,
>> -2.63454, 1.63098, 3.69696, 0.404995, 0.480342, 3.22724, -3.57127, -2.38176,
>> -1.23267, 0.738668, 1.64966, 1.37331, -2.60132, -1.60081, 2.57359, -3.58266,
>> 1.32347, 3.24265, 3.81, 3.90706, -0.407994, 2.42083, 3.34477, 3.43151,
>> -1.08974, -2.93732, 2.39014, -1.36511, -0.101514, -1.46445, 2.11849,
>> -3.63955, -1.57038, 3.41777, -1.00185, -0.0702487, 2.01317, -3.38133,
>> 3.64754, -0.740182, -3.64028, -3.77238, 2.45613, -3.11631, 3.82543, 2.15285,
>> -0.790691, -1.22153, -0.943069, -3.37327, 1.19097, 1.48834, 0.502127,
>> -2.90383, -3.4236, -0.676889, 3.41785, 2.54728, -2.60006, -3.25969,
>> -1.85346, -2.8088, 3.3905, -1.34015, -1.3877, 2.38485, 3.16688, -3.26326,
>> -1.94801, 0.0878641, 0.492529, 2.62313, -2.08994, -1.77721, 1.92357,
>> 0.739532, 0.869021, -3.82981, 3.92422, -1.16293, 3.82139, -1.67119, 1.1145,
>> -2.24382, -1.93777, -0.109559, -0.350947, 1.94832, -2.54192, 1.224,
>> 0.797731, 0.767982, -2.93565, -2.72896, 1.2624, 1.91513, -3.96412, 3.43534,
>> 0.358804, 3.05541, -0.213663, 0.38204, -0.539063, -0.897154, -2.91298,
>> -0.198784, -0.0732228, 2.99983, 3.54078, 2.27245, 3.87904, 2.99445,
>> -0.705307, 0.187173, 1.79102, 1.69581, 2.08613, 1.54021, 0.7471, -1.19008,
>> 2.44732, -1.59312, 1.5387, -0.526756, 3.06958, -1.707, -2.46148, -0.523427,
>> -0.675584, -3.02611, -2.22116, -3.4546, -2.94353, 2.1346, 3.51197, 1.85137,
>> 1.7461, -0.875901, -2.13891, -2.1714, 1.6953, -0.159958, 1.77583, -0.808156,
>> 2.04446, 3.58507, -1.27303, -0.0739294, 0.22885, -1.16883, -0.0437807,
>> -1.30141, 2.71702, 2.85379, 3.74969, 3.5839, -0.159889, -0.236555, 2.78411,
>> 2.15217, -0.945737, -1.90692, 0.536403, -1.08419, -3.75986, 2.65243,
>> -2.29661, 3.8776, 1.23146, -2.26545, 2.79205, 2.34152, -3.62388, -3.51983,
>> -0.152083, -0.77672, -0.0661756, -1.12531, 1.77691, -1.49266, -0.401453,
>> -2.98782, 1.15182, 3.00211, -0.338523, 2.63385, -1.30166, -1.96304,
>> -2.03665, -2.91373, 3.33512, 0.26508, -2.4008, -0.989122, -1.96516,
>> 0.498154, -0.139963, 1.762, -0.36494, 2.42886, 1.26076, -0.344707, -2.2629,
>> 3.01517, -0.192693, 1.72579, -3.09541, 0.898774, -3.33187, -2.09473,
>> 2.13997, -1.20736, -1.78102, 0.661333, -2.15738, -2.82721, -0.34423,
>> 0.945198, -1.3919, 2.24165, -1.72333, -3.61333, 0.177856, -0.499845,
>> 1.08322, -0.57797, 1.32396, -0.580476, -0.990233, 3.13608, 0.2254, 2.44513,
>> -1.43021, -2.20293, -0.0295935, 3.9359, 0.872028, 2.94495, 2.3334, -1.4539,
>> -2.0155, 1.90474, -1.83284, -3.6983, -0.223583, -2.19197, 2.98892, 2.11877,
>> -0.614374, 0.860207, 3.63726, -1.54793, 0.699044, -3.31199, -2.87789,
>> 3.21311, -3.24507, -0.0689166, 0.225146, -2.84127, -3.67944, 0.763724,
>> -3.93721, -3.81518, -1.06853, 0.726999, 0.562243, 3.79879, 3.75762, 2.1455,
>> 2.00329, -0.400098, -1.80113, 3.49374, 3.26726, -1.24347, 2.0535, 2.55697,
>> 0.670452, -2.79004, 1.39668, 2.32366, -2.27311, -0.352436, -2.71256,
>> -2.31389, -2.11829, 0.111656, -1.67798, 2.97944, -3.7505, -1.88802, 3.50199,
>> 1.31453, 3.32241, -1.04754, -3.03124, 1.60895, 1.15746, 2.29443, 3.31704,
>> -0.172815, 2.81695, 0.253896, 0.298466, -3.90939, -2.39831, 3.46711,
>> 2.41166, 2.03439, 0.387814, -3.40236, -3.71227, -1.68499, -3.81028, 2.97335,
>> 3.32693, -3.88281, -2.61789, -3.31616, 2.71789, 3.05144, -0.579528,
>> -0.672907, 2.75653);quartz(width=4, height=4, type="pdf",
>> file="~/Desktop/testpdf.pdf");plot(x=x, y=y, xlim=c(-5, 5), ylim=c(-5, 5),
>> pch=19, cex=0.5, main="2000");dev.off();}’
>>
>> If I execute the R code that is in the -e argument directly in R GUI (on OS
>> X) it works fine. And if I put that code in a file and run Rscript <file>,
>> it works fine. So the length limit is not intrinsic to R’s parser, it would
>> seem. But if I try to execute exactly the same code in an interactive R
>> session in my Unix terminal's command line, I get a continuation prompt, +,
>> and a little investigation indicates that the input line may have been
>> truncated after 3843 characters (a strange number) and it is waiting for
>> more input to follow that truncated input. And – what is most relevant for
>> my situation – if I try to run the full Rscript command as given above
>> (inside /bin/sh), it prints out:
>>
>> WARNING: '-e
>> {x~+~<-~+~c(-1.31171,~+~-0.686165,~+~1.62771,~+~0.320195,~+~-0.322011,~+~1.66518,~+~-0.271971,~+~-0.665367,~+~0.516482,~+~-0.716343,~+~-0.317471,~+~0.068046,~+~-0.100371,~+~-1.15907,~+~0.263329,~+~-0.936049,~+~-0.852444,~+~0.358817,~+~-0.233959,~+~0.209891,~+~-0.831575,~+~-0.952987,~+~-0.0420206,~+~-1.78527,~+~-0.280584,~+~-0.62353,~+~1.42597,~+~0.127994,~+~0.0751232,~+~0.896835,~+~-0.319488,~+~0.897876,~+~0.18457,~+~0.779571,~+~-0.0543194,~+~0.226722,~+~-0.769983,~+~-0.723463,~+~0.144386,~+~-0.468544,~+~-0.349417,~+~0.336786,~+~0.749212,~+~-1.62397,~+~0.683075,~+~-0.746449,~+~0.300921,~+~-0.365468,~+~0.548271,~+~1.13169,~+~-1.34042,~+~-0.0740572,~+~1.34986,~+~0.531771,~+~-0.147157,~+~0.824894,~+~-1.05816,~+~1.58867,~+~-0.885764,~+~1.11912,~+~0.361512,~+~1.77985,~+~0.585099,~+~-1.205,~+~2.44134,~+~-0.331372,~+~-0.346322,~+~0.0535267,~+~-1.75089,~+~0.0773243,~+~-1.07846,~+~-1.29632,~+~1.0622,~+~1.34867,~+~0.199777,~+~0.197516,~+~0.574185,~+~1.06555,~+~-0.885166,~+~-0.788576,~+~-1.46061,~+~-1.5402
>>
>> and then it hangs – the full warning doesn’t complete printing, so it is not
>> clear what it is trying to warn about. That represents 844 characters of
>> input script, but with the weird way that spaces have been replaced by ~+~
>> by somebody, it is 1013 characters – suspiciously close to 1024.
>>
>> Note that if I simply make the R script shorter, by plotting 100 x/y values
>> instead of 500, everything works fine. So there is no issue with the way
>> that I’m quoting strings or anything like that; the only issue seems to be
>> the total length of the command line.
>>
>> Now of course I could break up the script into multiple chunks, passed via
>> separate -e arguments, and perhaps that would work somewhat better. But
>> given that I want to set up a vector x with a single c() command containing
>> all of the data for x, I will still hit a line length limit; the single line
>> of code to set up x will already be over the maximum line length that
>> Rscript allows for a -e argument, apparently. Getting around that would
>> obviously be possible too, but would be considerably more hassle.
>>
>> And incidentally, this seems to have nothing to do with the /bin/sh input
>> line limit; that is much higher. According to "getconf ARG_MAX”, it is
>> 262144 characters on my machine, which is more than enough headroom for what
>> I’m trying to do.
>>
>> So my questions are: (1) is this a bug, (2) if so, do you think you are
>> likely to fix it any time soon :->, and (3) if the answer to that is no, are
>> there any standard workarounds for this sort of situation that you would
>> recommend? I suppose I could write out the script to a file and then
>> execute that file with Rscript, since that seems to work; but I was really
>> hoping to avoid that extra complication and overhead. Is there a better way?
>>
>> Thanks for any help you can provide! :->
>>
>> Cheers,
>> -B.
>>
>> Benjamin C. Haller
>> Messer Lab
>> Cornell University
>>
>> ______________________________________________
>> 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.
>
> Ben Tupper
> Bigelow Laboratory for Ocean Sciences
> 60 Bigelow Drive, P.O. Box 380
> East Boothbay, Maine 04544
> http://www.bigelow.org
>
> ______________________________________________
> 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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