R: Pander sink stack full when printing summary lm

Question

I am in the middle of generating a HTML report in Rstudio via pandoc for a collaborator. However pander is hitting the sink limit in R when trying to generate the output for the following summary of a lm() object.

My R instance:

version _
platform x86_64-apple-darwin13.1.0
arch x86_64
os darwin13.1.0
system x86_64, darwin13.1.0
status
major 3
minor 1.0
year 2014
month 04
day 10
svn rev 65387
language R
version.string R version 3.1.0 (2014-04-10) nickname Spring Dance

---

The lm I am trying to generate the HTML from:

summary(a.lm)

Call:
lm(formula = f.t ~ ((b.c + I(a.c^2) + b.t.c + 
    c.c) * (PTGENDER + DX.bl + Al1.Al2)) + BMI.t.c + FH.t.c + 
    Hb.t.c + age.c + I(age.c^2), data = subset(d, 
    !is.na(Hb.t.c) & !is.na(BMI.t.c) & !is.na(b.t.c) & !is.na(c.c)))

Residuals:
     Min       1Q   Median       3Q      Max 
-0.72042 -0.15865 -0.01311  0.15826  0.91421 

Coefficients:
                             Estimate Std. Error t value Pr(>|t|)    
(Intercept)                 1.6247957  0.1120717  14.498  < 2e-16 ***
a.c                         0.1343279  0.1481459   0.907  0.36541    
I(a.c^2)                   -0.0312254  0.0537683  -0.581  0.56193    
b.t.c                       0.1040226  0.0782932   1.329  0.18516    
c.c                         0.2012898  0.0818699   2.459  0.01461 *  
PTGENDERFemale              0.0067323  0.0473586   0.142  0.88707    
DX.blLMCI                  -0.0121387  0.0553348  -0.219  0.82654    
DX.blAD                     0.0209534  0.0769331   0.272  0.78557    
Al1.Al23:3                  0.1658594  0.1075438   1.542  0.12426    
Al1.Al23:4                  0.3506150  0.1121648   3.126  0.00198 ** 
Al1.Al24:4                  0.1386058  0.1690946   0.820  0.41316    
BMI.t.c                    -0.0280475  0.0182582  -1.536  0.12574    
FH.t.c                      0.0031254  0.0225851   0.138  0.89005    
Hb.t.c                      0.0162085  0.0171502   0.945  0.34551    
age.c                       0.0024730  0.0028751   0.860  0.39052    
I(age.c^2)                  0.0003961  0.0002926   1.354  0.17706    
a.c:PTGENDERFemale          0.0303573  0.0474341   0.640  0.52276    
a.c:DX.blLMCI               0.1143316  0.0603606   1.894  0.05934 .  
a.c:DX.blAD                 0.1406856  0.0691761   2.034  0.04302 *  
a.c:Al1.Al23:3             -0.0369030  0.1472692  -0.251  0.80234    
a.c:Al1.Al23:4             -0.0493593  0.1469924  -0.336  0.73730    
a.c:Al1.Al24:4             -0.0688362  0.1564964  -0.440  0.66041    
I(a.c^2):PTGENDERFemale    -0.0584777  0.0324483  -1.802  0.07270 .  
I(a.c^2):DX.blLMCI          0.0298364  0.0368905   0.809  0.41940    
I(a.c^2):DX.blAD            0.0147823  0.0440503   0.336  0.73747    
I(a.c^2):Al1.Al23:3         0.0001684  0.0586422   0.003  0.99771    
I(a.c^2):Al1.Al23:4        -0.0357507  0.0621727  -0.575  0.56578    
I(a.c^2):Al1.Al24:4        -0.0328713  0.0664954  -0.494  0.62149    
b.t.c:PTGENDERFemale        0.0208930  0.0466606   0.448  0.65470    
b.t.c:DX.blLMCI            -0.0640037  0.0628767  -1.018  0.30968    
b.t.c:DX.blAD              -0.0607185  0.0705763  -0.860  0.39042    
b.t.c:Al1.Al23:3           -0.0428761  0.0727674  -0.589  0.55624    
b.t.c:Al1.Al23:4           -0.0289522  0.0729465  -0.397  0.69178    
b.t.c:Al1.Al24:4           -0.0946543  0.0981224  -0.965  0.33564    
c.c:PTGENDERFemale          0.0193275  0.0445454   0.434  0.66474    
c.c:DX.blLMCI              -0.0371738  0.0470631  -0.790  0.43034    
c.c:DX.blAD                -0.1221799  0.0722145  -1.692  0.09189 .  
c.c:Al1.Al23:3             -0.1604799  0.0798383  -2.010  0.04548 *  
c.c:Al1.Al23:4             -0.2015401  0.0871098  -2.314  0.02149 *  
c.c:Al1.Al24:4             -0.3374309  0.1520609  -2.219  0.02737 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Residual standard error: 0.2795 on 254 degrees of freedom
Multiple R-squared:  0.4536,    Adjusted R-squared:  0.3697 
F-statistic: 5.406 on 39 and 254 DF,  p-value: < 2.2e-16

running:

pander(summary(a.lm))

leads to the following error

Error in sink(file) : sink stack is full

Any suggestions to overcome this would be much appreciated.

Cheers

---

In response to Mr Flick

Yes it seems to:

Here is an example:

d <- data.frame(a = rnorm(20), b = sample(letters[1:2], 20, replace = TRUE))
pander(summary(lm(a ~ b, data = d)))
Error in sink(file) : sink stack is full
pander(lm(a ~ b, data = d))
--------------------------------------------------------------
     &nbsp;        Estimate   Std. Error   t value   Pr(>|t|) 
----------------- ---------- ------------ --------- ----------
     **bb**        -0.1637      0.3797     -0.4311    0.6715  

 **(Intercept)**   -0.1634      0.2401     -0.6805    0.5049  
--------------------------------------------------------------

Table: Fitting linear model: a ~ b

So dropping the summary call works :)

Answer 1

Actually, if you're just running a standard lm regression, don't pass the summary.lm object to pander, pass the model itself (the lm object)

pander(a.lm)

That should have the information you need. The function calls summary() internally.